[med-svn] [mcl] 03/08: New upstream version 14-137+ds
Andreas Tille
tille at debian.org
Mon Jan 22 11:04:59 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mcl.
commit cc86e813d202cbb02cb9cc2351fa9cd4c4d286f2
Author: Andreas Tille <tille at debian.org>
Date: Mon Jan 22 11:45:44 2018 +0100
New upstream version 14-137+ds
---
Makefile.in | 704 ---------
doc/Makefile.in | 804 ----------
doc/clm.1 | 147 --
doc/clm.html | 226 ---
doc/clm.ps | 349 -----
doc/clmclose.1 | 144 --
doc/clmclose.html | 226 ---
doc/clmclose.ps | 366 -----
doc/clmdist.1 | 409 ------
doc/clmdist.html | 454 ------
doc/clmdist.ps | 828 -----------
doc/clmformat.1 | 627 --------
doc/clmformat.html | 674 ---------
doc/clmformat.ps | 1039 -------------
doc/clmimac.1 | 120 --
doc/clmimac.html | 214 ---
doc/clmimac.ps | 338 -----
doc/clminfo.1 | 187 ---
doc/clminfo.html | 262 ----
doc/clminfo.ps | 441 ------
doc/clminfo2.1 | 199 ---
doc/clminfo2.html | 264 ----
doc/clminfo2.ps | 426 ------
doc/clmmate.1 | 146 --
doc/clmmate.html | 218 ---
doc/clmmate.ps | 360 -----
doc/clmmeet.1 | 74 -
doc/clmmeet.html | 173 ---
doc/clmmeet.ps | 281 ----
doc/clmoptics.1 | 145 --
doc/clmoptics.html | 218 ---
doc/clmoptics.ps | 376 -----
doc/clmorder.1 | 87 --
doc/clmorder.html | 182 ---
doc/clmorder.ps | 310 ----
doc/clmprotocols.html | 435 ------
doc/clmprotocols.ps | 781 ----------
doc/clmprotocols2.html | 521 -------
doc/clmprotocols2.ps | 744 ----------
doc/clmresidue.1 | 96 --
doc/clmresidue.html | 196 ---
doc/clmresidue.ps | 309 ----
doc/clmvol.1 | 81 -
doc/clmvol.html | 178 ---
doc/clmvol.ps | 294 ----
doc/distindex.html | 199 ---
doc/index.html | 199 ---
doc/mcl.1 | 1569 --------------------
doc/mcl.html | 1522 -------------------
doc/mcl.ps | 2521 --------------------------------
doc/mclblastline.html | 227 ---
doc/mclblastline.ps | 401 -----
doc/mclcm.1 | 337 -----
doc/mclcm.html | 404 -----
doc/mclcm.ps | 655 ---------
doc/mclfamily.html | 245 ----
doc/mclfamily.ps | 306 ----
doc/mclfaq.html | 1487 -------------------
doc/mclfaq.ps | 2299 -----------------------------
doc/mclindex.ps | 300 ----
doc/mclpipeline.1 | 551 -------
doc/mclpipeline.html | 620 --------
doc/mclpipeline.ps | 891 -----------
doc/mcx.1 | 134 --
doc/mcx.html | 219 ---
doc/mcx.ps | 340 -----
doc/mcxalter.1 | 112 --
doc/mcxalter.html | 210 ---
doc/mcxalter.ps | 298 ----
doc/mcxarray.1 | 495 -------
doc/mcxarray.html | 437 ------
doc/mcxarray.ps | 685 ---------
doc/mcxassemble.1 | 560 -------
doc/mcxassemble.html | 522 -------
doc/mcxassemble.ps | 841 -----------
doc/mcxclcf.1 | 157 --
doc/mcxclcf.html | 215 ---
doc/mcxclcf.ps | 357 -----
doc/mcxconvert.1 | 114 --
doc/mcxconvert.html | 209 ---
doc/mcxconvert.ps | 345 -----
doc/mcxctty.1 | 195 ---
doc/mcxctty.html | 253 ----
doc/mcxctty.ps | 411 ------
doc/mcxdeblast.html | 303 ----
doc/mcxdeblast.ps | 452 ------
doc/mcxdiameter.1 | 172 ---
doc/mcxdiameter.html | 224 ---
doc/mcxdiameter.ps | 384 -----
doc/mcxdump.1 | 434 ------
doc/mcxdump.html | 452 ------
doc/mcxdump.ps | 730 ---------
doc/mcxerdos.1 | 173 ---
doc/mcxerdos.html | 260 ----
doc/mcxerdos.ps | 423 ------
doc/mcxi.1 | 349 -----
doc/mcxi.html | 460 ------
doc/mcxi.ps | 680 ---------
doc/mcxio.html | 780 ----------
doc/mcxio.ps | 1172 ---------------
doc/mcxload.1 | 583 --------
doc/mcxload.html | 589 --------
doc/mcxload.ps | 956 ------------
doc/mcxmap.1 | 223 ---
doc/mcxmap.html | 281 ----
doc/mcxmap.ps | 401 -----
doc/mcxquery.1 | 309 ----
doc/mcxquery.html | 372 -----
doc/mcxquery.ps | 588 --------
doc/mcxrand.1 | 236 ---
doc/mcxrand.html | 304 ----
doc/mcxrand.ps | 530 -------
doc/mcxsubs.1 | 605 --------
doc/mcxsubs.html | 682 ---------
doc/mcxsubs.ps | 947 ------------
doc/tingea.log.html | 213 ---
doc/tingea.log.ps | 448 ------
graphs/Makefile.in | 389 -----
img/Makefile.in | 382 -----
img/fa.ps | 1814 -----------------------
img/falkner-bidi.ps | 1606 --------------------
img/falkner.ps | 678 ---------
img/small.ps | 162 --
include/Makefile.in | 537 -------
scripts/Makefile.in | 405 -----
src/Makefile.in | 534 -------
src/alien/Makefile.in | 535 -------
src/alien/oxygen/Makefile.in | 535 -------
src/alien/oxygen/doc/Makefile.in | 481 ------
src/alien/oxygen/doc/mclblastline.1 | 136 --
src/alien/oxygen/doc/mclblastline.html | 227 ---
src/alien/oxygen/doc/mclblastline.ps | 401 -----
src/alien/oxygen/doc/mcxdeblast.1 | 193 ---
src/alien/oxygen/doc/mcxdeblast.html | 303 ----
src/alien/oxygen/doc/mcxdeblast.ps | 452 ------
src/alien/oxygen/src/Makefile.in | 395 -----
src/clew/Makefile.in | 443 ------
src/gryphon/Makefile.in | 439 ------
src/impala/Makefile.in | 453 ------
src/mcl/Makefile.in | 451 ------
src/shcl/Makefile.in | 609 --------
src/shmcl/Makefile.in | 486 ------
src/shmcx/Makefile.in | 481 ------
src/shmcxquery/Makefile.in | 437 ------
src/shmx/Makefile.in | 639 --------
testing/Makefile.in | 534 -------
testing/blast/Makefile.in | 338 -----
testing/setops/Makefile.in | 338 -----
testing/stream/Makefile.in | 338 -----
util/Makefile.in | 461 ------
150 files changed, 69822 deletions(-)
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diff --git a/doc/clm.1 b/doc/clm.1
deleted file mode 100644
index e89871a..0000000
--- a/doc/clm.1
+++ /dev/null
@@ -1,147 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm" 1 "16 May 2014" "clm 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
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-..
-.de ZJ
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-.\" Zoem Indent/Itemize macro II.
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-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm \- perform various computations on graphs and clusterings
-.SH SYNOPSIS
-
-.di ZV
-.in 0
-.nf \fC
- \fBclm\fP <mode> [mode-options] [mode-files]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.SH DESCRIPTION
-
-\fBclm\fP implements a variety of computations on graphs and clusterings\&. The
-first argument to \fBclm\fP should be a \fImode\fP, which is a string establishing
-the type of computation to invoke\&. Each mode \fImode\fP is described in the
-clm\fImode\fP manual page\&. The currently available modes are
-\fBclm\ \&dist\fP,
-\fBclm\ \&info\fP,
-\fBclm\ \&meet\fP,
-\fBclm\ \&mate\fP,
-\fBclm\ \&close\fP,
-\fBclm\ \&order\fP,
-\fBclm\ \&imac\fP,
-\fBclm\ \&vol\fP, and
-\fBclm\ \&residue\fP\&.
-The \fBdist\fP mode is thus described in the
-\fBclmdist\fP manual page\&.
-
-Invoking \fBclm\fP without arguments causes it to print out a list
-of available modes with a short description of the type of
-command line expected by that mode\&.
-
-Invoking \fBclm\fP with just a mode will print out a longer listing
-of options available for that particular mode\&.
-Modes that are able to function normally without arguments
-can be invoked by adding the \fI--nop\fP argument\&.
-
-Several options are shared between all \fBclm\fP modes\&. Note that
-these options are specified after the \fBmode\fP\&. See \fBOPTIONS\fP\&.
-
-The \fB--version\fP option causes \fBclm\fP to print out version
-and license information\&.
-
-Issuing \fIclm help mode\fP will cause \fBclm\fP to look for a manual page
-describing \fImode\fP and display it if found\&. This requires that the
-MANPATH environment variable contains the directory in which the MCL-edge
-manual pages were installed\&. This will usually be \fCPREFIX/share\fP,
-where \fCPREFIX\fP is the path with which the software was configured\&.
-.SH OPTIONS
-
-These are options that pertain to all modes\&. They should be specified
-\fIafter\fP the mode argument\&.
-
-.ZI 2m "\fB-h\fP (\fIsynopsis\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--help\fP (\fIsynopsis\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-List available options\&.
-.in -2m
-
-.ZI 2m "\fB--nop\fP (\fIno-op\fP)"
-\&
-.br
-Not an option\&. This option has no effect then to increment
-the argument count\&. This can be useful for \fBclm\fP modes which are able to
-function without any options\&. Such a mode typically reads from STDIN, writes
-to STDOUT, and uses default settings\&. However, simply specifying a mode
-without options leads \fBclm\fP to output a list of available options for that
-mode\&. This can be averted by using the \fB--nop\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-set\fP key=val (\fIset key-value pair\fP)"
-\&
-.br
-Sets the key\ \&\fBkey\fP to value\ \&\fBval\fP in the environment\&.
-Some modes allow adjustment of settings in this manner\&.
-.in -2m
-
-.ZI 2m "\fB-debug\fP <int> (\fIset debug level/flags\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--debug\fP (\fIturn default debugging on\fP)"
-\&
-'in -2m
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-\&
-'in -2m
-'in +2m
-\&
-.br
-The first two turn on debugging, the last is for testing\&. The effect of
-these options is otherwise undocumented\&.
-.in -2m
-
-.ZI 2m "\fB--progress\fP (\fIenable progress reporting\fP)"
-\&
-.br
-This will enable some kind of progress reporting, by
-writing to STDERR\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clm.html b/doc/clm.html
deleted file mode 100644
index 29a8ee7..0000000
--- a/doc/clm.html
+++ /dev/null
@@ -1,226 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
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-{ text-align: justify;
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-{ font-family: monospace;
-margin-top: 1em;
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-{ margin-left: 8%;
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-{ position: relative;
-margin-left: 8%;
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-{ width: 2em;
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-body
-{ text-align: justify;
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-</style>
-<title>The clm manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clm.ps"><b>clm</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm — perform various computations on graphs and clusterings</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<div class="verbatim"> <b>clm</b> <mode> [mode-options] [mode-files]</div>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm</b> implements a variety of computations on graphs and clusterings. The
-first argument to <b>clm</b> should be a <i>mode</i>, which is a string establishing
-the type of computation to invoke. Each mode <i>mode</i> is described in the
-clm<i>mode</i> manual page. The currently available modes are
-<a class="local sibling" href="clmdist.html">clm dist</a>,
-<a class="local sibling" href="clminfo.html">clm info</a>,
-<a class="local sibling" href="clmmeet.html">clm meet</a>,
-<a class="local sibling" href="clmmate.html">clm mate</a>,
-<a class="local sibling" href="clmclose.html">clm close</a>,
-<a class="local sibling" href="clmorder.html">clm order</a>,
-<a class="local sibling" href="clmimac.html">clm imac</a>,
-<a class="local sibling" href="clmvol.html">clm vol</a>, and
-<a class="local sibling" href="clmresidue.html">clm residue</a>.
-The <b>dist</b> mode is thus described in the
-<a class="local sibling" href="clmdist.html">clmdist</a> manual page.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Invoking <b>clm</b> without arguments causes it to print out a list
-of available modes with a short description of the type of
-command line expected by that mode.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Invoking <b>clm</b> with just a mode will print out a longer listing
-of options available for that particular mode.
-Modes that are able to function normally without arguments
-can be invoked by adding the <i>--nop</i> argument.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Several options are shared between all <b>clm</b> modes. Note that
-these options are specified after the <b>mode</b>. See <a class="intern" href="#options">OPTIONS</a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--version</b> option causes <b>clm</b> to print out version
-and license information.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Issuing <i>clm help mode</i> will cause <b>clm</b> to look for a manual page
-describing <i>mode</i> and display it if found. This requires that the
-MANPATH environment variable contains the directory in which the MCL-edge
-manual pages were installed. This will usually be <tt>PREFIX/share</tt>,
-where <tt>PREFIX</tt> is the path with which the software was configured.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<p style="margin-bottom:0" class="asd_par">
-These are options that pertain to all modes. They should be specified
-<i>after</i> the mode argument.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade item_leftalign nowrap" ><a name="opt-h"></a><b>-h</b> (<i>synopsis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--help"></a><b>--help</b> (<i>synopsis</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-List available options.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--nop"></a><b>--nop</b> (<i>no-op</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Not an option. This option has no effect then to increment
-the argument count. This can be useful for <b>clm</b> modes which are able to
-function without any options. Such a mode typically reads from STDIN, writes
-to STDOUT, and uses default settings. However, simply specifying a mode
-without options leads <b>clm</b> to output a list of available options for that
-mode. This can be averted by using the <b>--nop</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-set"></a><b>-set</b> key=val (<i>set key-value pair</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sets the key <b>key</b> to value <b>val</b> in the environment.
-Some modes allow adjustment of settings in this manner.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-debug"></a><b>-debug</b> <int> (<i>set debug level/flags</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--debug"></a><b>--debug</b> (<i>turn default debugging on</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--test"></a><b>--test</b> (<i>turn default testing on</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The first two turn on debugging, the last is for testing. The effect of
-these options is otherwise undocumented.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--progress"></a><b>--progress</b> (<i>enable progress reporting</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This will enable some kind of progress reporting, by
-writing to STDERR.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
diff --git a/doc/clm.ps b/doc/clm.ps
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diff --git a/doc/clmclose.1 b/doc/clmclose.1
deleted file mode 100644
index 3b46fcd..0000000
--- a/doc/clmclose.1
+++ /dev/null
@@ -1,144 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm close" 1 "16 May 2014" "clm close 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm close \- Fetch connected components from graphs or subgraphs
-
-clmclose is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIclose\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm close\fP -imx <fname> [options]
-
-\fBclm close\fP
-\fB-imx\fP fname (\fIspecify matrix input\fP)
-\fB-abc\fP fname (\fIspecify label input\fP)
-\fB-dom\fP fname (\fIinput domain/cluster file\fP)
-\fB[-o\fP fname (\fIoutput file\fP)\fB]\fP
-\fB[--is-undirected\fP (\fItrust input graph to be undirected\fP)\fB]\fP
-\fB[--write-count\fP (\fIoutput component count\fP)\fB]\fP
-\fB[--write-sizes\fP (\fIoutput component sizes (default)\fP)\fB]\fP
-\fB[--write-cc\fP (\fIoutput components as clustering\fP)\fB]\fP
-\fB[--write-block\fP (\fIoutput graph restricted to -dom argument\fP)\fB]\fP
-\fB[--write-blockc\fP (\fIoutput graph complement of -dom argument\fP)\fB]\fP
-\fB[-cc-bound\fP num (\fIselect components with size at least num\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-Use \fBclm close\fP to fetch the connected components from a graph\&. Different
-output modes are supported (see below)\&. In matrix mode (i\&.e\&. using
-the \fB-imx\fP option) the output returned with
-\fB--write-cc\fP can be used in conjunction with \fBmcxsubs\fP
-to retrieve individual subgraphs corresponding to connected components\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input that is in mcl native matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
-\&
-.br
-Specify the file where output is sent to\&. The default is STDOUT\&.
-.in -2m
-
-.ZI 2m "\fB-dom\fP fname (\fIinput domain/cluster file\fP)"
-\&
-.br
-If this option is used, clm close will, as a first step,
-for each of the domains in file\ \&\fIfname\fP retrieve the associated
-subgraph from the input graph\&. These are then further decomposed into
-connected components, and the program will process these in the normal
-manner\&.
-.in -2m
-
-.ZI 2m "\fB--write-count\fP (\fIoutput component count\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-sizes\fP (\fIoutput component sizes (default)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-cc\fP (\fIoutput components as clustering\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-block\fP (\fIoutput graph restricted to -dom argument\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-blockc\fP (\fIoutput graph complement of -dom argument\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The default behaviour is currently to output the sizes of the
-connected components\&. It is also possible to simply output
-the number of components with \fB--write-count\fP or to
-write the components as a clustering in mcl format with
-\fB-write-cc\fP\&. Even more options exist: it is possible
-to output the restriction of the input graph to a domain, or
-to output the complement of this restriction\&.
-.in -2m
-
-.ZI 2m "\fB--is-undirected\fP (\fIomit graph undirected check\fP)"
-\&
-.br
-With this option the transformation to make sure
-that the input is undirected is omitted\&. This will
-be slightly faster\&. Using this option while the
-input is directed may lead to erronenous results\&.
-.in -2m
-
-.ZI 2m "\fB-cc-bound\fP num (\fIselect components with size at least num\fP)"
-\&
-.br
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmclose.html b/doc/clmclose.html
deleted file mode 100644
index 33c367b..0000000
--- a/doc/clmclose.html
+++ /dev/null
@@ -1,226 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
-margin-right: 0%;
-}
-a:link { text-decoration: none; }
-a:active { text-decoration: none; }
-a:visited { text-decoration: none; }
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-<title>The clm close manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmclose.ps"><b>clm close</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm close — Fetch connected components from graphs or subgraphs</p>
-<p style="margin-bottom:0" class="asd_par">clmclose is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>close</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm close</b> -imx <fname> [options]
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm close</b>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>specify matrix input</i>)</a>
-<a class="intern" href="#opt-abc"><b>-abc</b> fname (<i>specify label input</i>)</a>
-<a class="intern" href="#opt-dom"><b>-dom</b> fname (<i>input domain/cluster file</i>)</a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file</i>)<b>]</b></a>
-<a class="intern" href="#opt--is-undirected"><b>[--is-undirected</b> (<i>trust input graph to be undirected</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-count"><b>[--write-count</b> (<i>output component count</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-sizes"><b>[--write-sizes</b> (<i>output component sizes (default)</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-cc"><b>[--write-cc</b> (<i>output components as clustering</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-block"><b>[--write-block</b> (<i>output graph restricted to -dom argument</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-blockc"><b>[--write-blockc</b> (<i>output graph complement of -dom argument</i>)<b>]</b></a>
-<a class="intern" href="#opt-cc-bound"><b>[-cc-bound</b> num (<i>select components with size at least num</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-Use <b>clm close</b> to fetch the connected components from a graph. Different
-output modes are supported (see below). In matrix mode (i.e. using
-the <b>-imx</b> option) the output returned with
-<b>--write-cc</b> can be used in conjunction with <b>mcxsubs</b>
-to retrieve individual subgraphs corresponding to connected components.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in mcl native matrix format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the file where output is sent to. The default is STDOUT.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dom"></a><b>-dom</b> fname (<i>input domain/cluster file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If this option is used, clm close will, as a first step,
-for each of the domains in file <i>fname</i> retrieve the associated
-subgraph from the input graph. These are then further decomposed into
-connected components, and the program will process these in the normal
-manner.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-count"></a><b>--write-count</b> (<i>output component count</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-sizes"></a><b>--write-sizes</b> (<i>output component sizes (default)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-cc"></a><b>--write-cc</b> (<i>output components as clustering</i>)</div><div class=" item_casc [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The default behaviour is currently to output the sizes of the
-connected components. It is also possible to simply output
-the number of components with <b>--write-count</b> or to
-write the components as a clustering in mcl format with
-<b>-write-cc</b>. Even more options exist: it is possible
-to output the restriction of the input graph to a domain, or
-to output the complement of this restriction.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--is-undirected"></a><b>--is-undirected</b> (<i>omit graph undirected check</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-With this option the transformation to make sure
-that the input is undirected is omitted. This will
-be slightly faster. Using this option while the
-input is directed may lead to erronenous results.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cc-bound"></a><b>-cc-bound</b> num (<i>select components with size at least num</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/clmdist.1 b/doc/clmdist.1
deleted file mode 100644
index 510ad2f..0000000
--- a/doc/clmdist.1
+++ /dev/null
@@ -1,409 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm dist" 1 "16 May 2014" "clm dist 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm dist \- compute the distance between two or more partitions (clusterings)\&.
-
-The distance that is computed can be any of
-\fIsplit/join distance\fP, \fIvariance of information\fP,
-or \fIMirkin metric\fP\&.
-
-clmdist is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIdist\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm dist\fP [options] <file name> <file name>+
-
-\fBclm dist\fP
-\fB[-mode\fP <sj|vi|mk|sc> (\fIdistance type\fP)\fB]\fP
-\fB[-o\fP fname (\fIoutput file\fP)\fB]\fP
-\fB[--chain\fP (\fIonly compare consecutive clusterings\fP)\fB]\fP
-\fB[--one-to-many\fP (\fIcompare first clustering to all others\fP)\fB]\fP
-\fB[--sort\fP (\fIsort clusterings based on coarseness\fP)\fB]\fP
-\fB[--index\fP (\fIoutput Rand, adjusted Rand and Jaccard indices\fP)\fB]\fP
-\fB[-digits\fP k (\fIoutput decimals\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-<file name> <file name>+
-.SH DESCRIPTION
-
-\fBclm dist\fP computes distances between clusterings\&. It can compute the
-\fIsplit/join distance\fP (described below), the \fIvariance of information
-measure\fP, and the \fIMirkin metric\fP\&. By default it computes the chosen distance
-for all pairs of distances in the clusterings provided\&. Clusterings must be in
-the mcl matrix format (cf\&. \fBmcxio(5)\fP), and are supplied on the command
-line as the names of the files in which they are stored\&.
-It is possible to compare only consecutive clusterings by using
-the \fB--chain\fP option\&.
-
-Currently, \fBclm dist\fP cannot compute different distance types simultaneously\&.
-
-The output is linewise, each line giving information about
-the distance between a pair of clusterings\&. A line has the
-following format:
-
-.di ZV
-.in 0
-.nf \fC
-d d1 d2 N v name1 name2 [v50,v75,v90,v95,v99]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-where \fCdT\fP is the distance between the two clusterings, \fCd1\fP is the
-distance from the first clustering to the greatest common subclustering
-(alternatively called GCS, intersection, or meet) of the two clusterings,
-\fCd2\fP is similarly the distance from the second clustering to the GCS,
-\fCN\fP is the number of nodes in the set over which the clusterings are
-defined, \fCname1\fP is the name of the file containing the first clustering,
-\fCname2\fP is the name of the file containing the second clustering, and
-\fCvXX\fP is the number of \fIvolatile nodes\fP at stringency factor \fC0\&.XX\fP
-(i\&.e\&. 0\&.5 for \fCv50\fP)\&. Refer to \fBclm\ \&vol\fP for a definition of
-\fIvolatile node\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-mode\fP <sj|vi|mk> (\fIdistance type\fP)"
-\&
-.br
-Use \fBsj\fP for the \fIsplit/join distance\fP (described below), \fBvi\fP for
-the \fIvariance of information measure\fP and \fBmk\fP for the \fIMirkin metric\fP\&.
-.in -2m
-
-.ZI 2m "\fB--chain\fP (\fIonly compare consecutive clusterings\fP)"
-\&
-.br
-This option can be used if you know that the clusterings are nested
-clusterings (or appoximately so) and ordered from coarse to fine-grained
-or vice versa\&. An example of this is the set of clusterings resulting
-from applying \fBmcl\fP with a range of inflation parameters\&.
-.in -2m
-
-.ZI 2m "\fB--one-to-many\fP (\fIcompare first clustering to all others\fP)"
-\&
-.br
-Use this option for example to compare a gold standard classification
-to a collection of clusterings\&.
-Bear in mind that sub-clustering and super-clustering are also
-ways for a clustering to be compatible with a gold standard\&.
-This means that the simple numerical criterion of distance between
-clusters (by whatever method) is only partially informative\&.
-For the Mirkin, variation of information and split/join metrics
-it pays to take into account the constituent distances \fCd1\fP
-and \fCd2\fP (see above)\&. Assuming that the first clustering
-given as argument represents a gold standard, a small value
-for \fCd1\fP implies that the second clustering is (nearly) a superclustering,
-and similarly a small value for \fCd2\fP implies that it is (nearly)
-a subclustering\&.
-.in -2m
-
-.ZI 2m "\fB--sort\fP (\fIsort clusterings based on coarseness\fP)"
-\&
-.br
-This option can be useful in conjunction with the \fB--chain\fP
-option, in case the list of clusterings supplied is not necessarily
-ordered by granularity\&.
-.in -2m
-
-.ZI 2m "\fB--index\fP (\fIoutput Rand, adjusted Rand and Jaccard indices\fP)"
-\&
-.br
-As described\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-digits\fP k (\fIoutput decimals\fP)"
-\&
-.br
-The number of decimals printed when using the variance of information measure\&.
-.in -2m
-.SH SPLIT/JOIN DISTANCE
-
-For each pair of clusterings \fBC1\fP, \fBC2\fP, two numbers are given,
-say \fBd1\fP and \fBd2\fP\&. Then \fBd1\fP + \fBd2\fP equals the number
-of nodes that have to be exchanged in order to transform any of the two
-clusterings into the other, and you can think of (\fBd1\fP+\fBd2\fP)/\fB2N\fP
-as the percentage that the two clusterings differ\&. The split/join
-distance has a linearity property with respect to the meet of \fBC1\fP and
-\fBC2\fP, see below\&.
-
-The split/join distance \fBsjd\fP is very handy in computing the consistency of
-two or more clusterings of the same graph, or comparing clusterings made
-with different resource (but otherwise identical) parameters\&. The latter is
-for finding out whether you can settle for cheaper mcl settings, or whether
-you need to switch to more expensive settings\&. The former is for finding out
-whether clusterings are identical, conflicting, or whether one is (almost) a
-subclustering of the other - mostly for comparing a set of clusterings of
-different granularity, made by letting the mcl parameter \fB-I\fP vary\&.
-The \fBEXAMPLES\fP section contains examples of all these \fBclm dist\fP uses,
-and the use of \fBclm info\fP and \fBclm meet\fP is also discussed there\&.
-
-\fBsjd\fP is a metric distance on the space of partitions of
-a set of a given fixed cardinality\&. It has the following linearity
-property\&. Let \fBP1\fP and \fBP2\fP be partitions, then
-
-\fBsjd\fP(\fBP1\fP, \fBP2\fP) = \fBsjd\fP(\fBP1\fP, \fBD\fP) + \fBsjd\fP(\fBP2\fP, \fBD\fP)
-
-where \fBD\fP (for Dutch Doorsnede)
-is the intersection of \fBP1\fP and \fBP2\fP, i\&.e\&. the unique clustering
-that is both a subclustering of \fBP1\fP and \fBP2\fP \fIand\fP a superclustering of
-all other subclusterings of \fBP1\fP and \fBP2\fP\&. Sloppily worded, \fBD\fP is the largest
-subclustering of both \fBP1\fP and \fBP2\fP\&. See the \fBREFERENCES\fP section for
-a pointer to the technical report in which \fBsjd\fP was first defined (and in
-which the non-trivial triangle inequality is proven)\&.
-
-Because it is useful to know whether one partition (or clustering)
-is almost a subclustering of the other, \fBclm dist\fP returns the
-two constituents \fBsjd\fP(\fBP1\fP,\fBD\fP) and \fBsjd\fP(\fBP2\fP,\fBD\fP)\&.
-
-Let \fBP1\fP and \fBP2\fP be two clusterings of a graph of cardinality \fBN\fP,
-and suppose \fBclm dist\fP returns the integers \fBd1\fP and \fBd2\fP\&. You can think of
-\fB100 * (d1 + d2) / N\fP as the percentage that \fBP1\fP and \fBP2\fP differ\&.
-This interpretation is in fact slightly conservative\&.
-The numerator is the number of nodes that need to be exchanged in order to
-transform one into the other\&. This number may grow as large as
-\fB2*N - 2*sqrt(N)\fP, so it would be justified to take 50 as a scaling
-factor rather than 100\&.
-
-For example, if \fBA\fP and \fBB\fP are both clusterings of a graph
-on a set of 9058 nodes and \fBclm dist\fP returns [38, 2096], this conveys
-that \fBA\fP is almost a subclustering of \fBB\fP (by splitting 38 nodes
-in \fBA\fP we obtain a clustering \fBD\fP that is a subclustering of \fBB\fP),
-and that \fBB\fP is much less granular than \fBA\fP\&. The latter is
-because we can obtain \fBB\fP from \fBD\fP by \fIjoining\fP 2096 nodes
-in some way\&.
-.SH EXAMPLES
-
-The following is an example of several mcl validation tools
-applied to a set of clusterings on a protein graph of 9058 nodes\&.
-In the first experiment, six
-different clusterings were generated for different values of the inflation
-parameter, which was respectively set to 1\&.2, 1\&.6, 2\&.0, 2\&.4, 2\&.8, and 3\&.2\&.
-It should be noted that protein graphs seem somewhat special in that an
-inflation parameter setting as low as 1\&.2 still produces a very acceptable
-clustering\&. The six clusterings are scrutinized using \fBclm dist\fP,
-\fBclm info\fP, and \fBclm meet\fP\&.
-In the second experiment, four different clusterings were generated
-with identical flow (i\&.e\&. inflation) parameter, but
-with different resource parameters\&. \fBclm dist\fP is used to choose
-a sufficient resource level\&.
-
-High \fB-P/-S/-R\fP values make \fBmcl\fP more accurate but also
-more time and memory consuming\&. Run \fBmcl\fP with different settings for these
-parameters, holding other parameters fixed\&. If the expensive and supposedly
-more accurate clusterings are very similar to the clusterings resulting from
-cheaper settings, the cheaper setting is sufficient\&. If the distances
-between cheaper clusterings and more expensive clusterings are large, this
-is an indication that you need the expensive settings\&. In that case, you may
-want to increase the \fB-P/-S/-R\fP parameters (or simply the
-\fB-scheme\fP parameter) until associated
-clusterings at nearby resource levels are very similar\&.
-
-In this particular example, the validation tools do not reveal that one
-clustering in particular can be chosen as \&'best\&', because all clusterings
-seem at least acceptable\&. They do aid however in showing the relative
-merits of each clusterings\&. The most important issue in this respect is
-cluster granularity\&. The table below shows the output of \fBclm info\fP\&.
-
-.di ZV
-.in 0
-.nf \fC
-
- Efficiency Mass frac Area frac Cl weight Mx link weight
-1\&.2 0\&.42364 0\&.98690 0\&.02616 52\&.06002 50\&.82800
-1\&.6 0\&.58297 0\&.95441 0\&.01353 55\&.40282 50\&.82800
-2\&.0 0\&.63279 0\&.92386 0\&.01171 58\&.09409 50\&.82800
-2\&.4 0\&.65532 0\&.90702 0\&.01091 59\&.58283 50\&.82800
-2\&.8 0\&.66854 0\&.84954 0\&.00940 63\&.19183 50\&.82800
-3\&.2 0\&.67674 0\&.82275 0\&.00845 66\&.10831 50\&.82800
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This data shows that there is exceptionally strong cluster structure present
-in the input graph\&. The 1\&.2 clustering captures almost all edge mass using
-only 2\&.5 percent of \&'area\&'\&. The 3\&.2 clustering still captures 82 percent of
-the mass using less than 1 percent of area\&. We continue with looking at the
-mutual consistency of the six clusterings\&. Below is a table that shows all
-pairwise distances between the clusterings\&.
-
-.di ZV
-.in 0
-.nf \fC
-
- | 1\&.6 | 2\&.0 | 2\&.4 | 2\&.8 | 3\&.2 | 3\&.6
------------------------------------------------------------\&.
-1\&.2 |2096,38 |2728,41 |3045,48 |3404,45 |3621,43 |3800, 42 |
------------------------------------------------------------|
-1\&.6 | | 797,72 |1204,76 |1638,78 |1919,70 |2167, 69 |
------------------------------------------------------------|
-2\&.0 | | | 477,68 | 936,78 |1235,85 |1504, 88 |
------------------------------------------------------------|
-2\&.4 | | | | 498,64 | 836,91 |1124,103 |
------------------------------------------------------------|
-2\&.8 | | | | | 384,95 | 688,119 |
------------------------------------------------------------|
-3\&.2 | | | | | | 350,110 |
------------------------------------------------------------\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The table shows that the different clusterings are pretty consistent with
-each other, because for two different clusterings it is generally true that
-one is almost a subclustering of the other\&. The interpretation for the
-distance between the 1\&.6 and the 3\&.2 clustering for example, is that by
-rearranging 43 nodes in the 3\&.2 clustering, we obtain a subclustering of the
-1\&.6 clustering\&. The table shows that for any pair of clusterings, at most
-119 entries need to be rearranged in order to make one a subclustering of
-the other\&.
-
-The overall consistency becomes all the more clear by looking at the meet of
-all the clusterings:
-
-.di ZV
-.in 0
-.nf \fC
-
-clm meet -o meet out12 out16 out20 out24 out28 out32
-clm dist meet out12 out16 out20 out24 out28 out32
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-results in the following distances between the respective clusterings
-and their meet\&.
-
-.di ZV
-.in 0
-.nf \fC
-
- | 1\&.2 | 1\&.6 | 2\&.0 | 2\&.4 | 2\&.8 | 3\&.2 |
--------------- --------------------------------------------\&.
-meet| 0,3663| 0,1972| 0,1321 | 0,958 | 0,559 | 0,283 |
--------------- --------------------------------------------\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This shows that by rearranging only 283 nodes in the 3\&.2 clustering,
-one obtains a subclustering of all other clusterings\&.
-
-In the last experiment, \fBmcl\fP was run with inflation parameter 1\&.4,
-for each of the four different preset pruning schemes \fCk=1,2,3,4\fP\&.
-The \fBclm dist\fP distances between the different clusterings
-are shown below\&.
-
-.di ZV
-.in 0
-.nf \fC
-
- | k=2 | k=3 | k=4 |
--------------------------------\&.
-k=1 | 17,17 | 16,16 | 16,16 |
--------------------------------\&.
-k=2 | | 3,3 | 5,5 |
--------------------------------\&.
-k=3 | | | 4,4 |
--------------------------------\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This example is a little boring in that the cheapest scheme seems adequate\&.
-If anything, the gaps between the \fCk=1\fP scheme and the rest are a little
-larger than the three gaps between the \fCk=2\fP, \fCk=3\fP, and \fCk=4\fP
-clusterings\&. Had all distances been much larger, then such an observation
-would be reason to choose the \fCk=2\fP setting\&.
-
-Note that you need not feel uncomfortable with the clusterings
-still being different at high resource levels, if ever so slightly\&.
-In all likelihood, there are anyway nodes which are not in any core of
-attraction, and that are on the boundary between two or more clusterings\&.
-They may go one way or another, and these are the nodes which
-will go different ways even at high resource levels\&.
-Such nodes may be stable in clusterings obtained for lower inflation
-values (i\&.e\&. coarser clusterings), in which the different clusters
-to which they are attracted are merged\&.
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
-.SH REFERENCES
-
-Stijn van Dongen\&. \fIPerformance criteria for graph clustering and Markov
-cluster experiments\fP\&. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0012\&.ps\&.Z
-
-Marina Meila\&. \fIComparing Clusterings \- An Axiomatic View\fP\&.
-In \fIProceedings of the 22nd International Conference on Machine Learning\fP,
-Bonn, Germany, 2005\&.
-
-Marina Meila\&. \fIComparing Clusterings\fP,
-UW Statistics Technical Report 418\&.
-.br
-http://www\&.stat\&.washington\&.edu/www/research/reports/2002/tr418\&.ps
diff --git a/doc/clmdist.html b/doc/clmdist.html
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-<title>The clm dist manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmdist.ps"><b>clm dist</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#_section_5">SPLIT/JOIN DISTANCE</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#examples">EXAMPLES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm dist — compute the distance between two or more partitions (clusterings).</p>
-<p style="margin-bottom:0" class="asd_par">
-The distance that is computed can be any of
-<i>split/join distance</i>, <i>variance of information</i>,
-or <i>Mirkin metric</i>.</p>
-<p style="margin-bottom:0" class="asd_par">clmdist is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>dist</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm dist</b> [options] <file name> <file name>+</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm dist</b>
-<a class="intern" href="#opt-mode"><b>[-mode</b> <sj|vi|mk|sc> (<i>distance type</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file</i>)<b>]</b></a>
-<a class="intern" href="#opt--chain"><b>[--chain</b> (<i>only compare consecutive clusterings</i>)<b>]</b></a>
-<a class="intern" href="#opt--one-to-many"><b>[--one-to-many</b> (<i>compare first clustering to all others</i>)<b>]</b></a>
-<a class="intern" href="#opt--sort"><b>[--sort</b> (<i>sort clusterings based on coarseness</i>)<b>]</b></a>
-<a class="intern" href="#opt--index"><b>[--index</b> (<i>output Rand, adjusted Rand and Jaccard indices</i>)<b>]</b></a>
-<a class="intern" href="#opt-digits"><b>[-digits</b> k (<i>output decimals</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<file name> <file name>+</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm dist</b> computes distances between clusterings. It can compute the
-<i>split/join distance</i> (described below), the <i>variance of information
-measure</i>, and the <i>Mirkin metric</i>. By default it computes the chosen distance
-for all pairs of distances in the clusterings provided. Clusterings must be in
-the mcl matrix format (cf. <a class="local sibling" href="mcxio.html">mcxio</a>), and are supplied on the command
-line as the names of the files in which they are stored.
-It is possible to compare only consecutive clusterings by using
-the <b>--chain</b> option.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Currently, <b>clm dist</b> cannot compute different distance types simultaneously.</p>
-<p style="margin-bottom:0" class="asd_par">
-The output is linewise, each line giving information about
-the distance between a pair of clusterings. A line has the
-following format:</p>
-<div class="verbatim">d d1 d2 N v name1 name2 [v50,v75,v90,v95,v99]</div>
-<p style="margin-top:0em; margin-bottom:0em">
-where <tt>dT</tt> is the distance between the two clusterings, <tt>d1</tt> is the
-distance from the first clustering to the greatest common subclustering
-(alternatively called GCS, intersection, or meet) of the two clusterings,
-<tt>d2</tt> is similarly the distance from the second clustering to the GCS,
-<tt>N</tt> is the number of nodes in the set over which the clusterings are
-defined, <tt>name1</tt> is the name of the file containing the first clustering,
-<tt>name2</tt> is the name of the file containing the second clustering, and
-<tt>vXX</tt> is the number of <i>volatile nodes</i> at stringency factor <tt>0.XX</tt>
-(i.e. 0.5 for <tt>v50</tt>). Refer to <a class="local sibling" href="clmvol.html">clm vol</a> for a definition of
-<i>volatile node</i>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-mode"></a><b>-mode</b> <sj|vi|mk> (<i>distance type</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use <b>sj</b> for the <i>split/join distance</i> (described below), <b>vi</b> for
-the <i>variance of information measure</i> and <b>mk</b> for the <i>Mirkin metric</i>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--chain"></a><b>--chain</b> (<i>only compare consecutive clusterings</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option can be used if you know that the clusterings are nested
-clusterings (or appoximately so) and ordered from coarse to fine-grained
-or vice versa. An example of this is the set of clusterings resulting
-from applying <b>mcl</b> with a range of inflation parameters.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--one-to-many"></a><b>--one-to-many</b> (<i>compare first clustering to all others</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this option for example to compare a gold standard classification
-to a collection of clusterings.
-Bear in mind that sub-clustering and super-clustering are also
-ways for a clustering to be compatible with a gold standard.
-This means that the simple numerical criterion of distance between
-clusters (by whatever method) is only partially informative.
-For the Mirkin, variation of information and split/join metrics
-it pays to take into account the constituent distances <tt>d1</tt>
-and <tt>d2</tt> (see above). Assuming that the first clustering
-given as argument represents a gold standard, a small value
-for <tt>d1</tt> implies that the second clustering is (nearly) a superclustering,
-and similarly a small value for <tt>d2</tt> implies that it is (nearly)
-a subclustering.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--sort"></a><b>--sort</b> (<i>sort clusterings based on coarseness</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option can be useful in conjunction with the <b>--chain</b>
-option, in case the list of clusterings supplied is not necessarily
-ordered by granularity.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--index"></a><b>--index</b> (<i>output Rand, adjusted Rand and Jaccard indices</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-As described.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-digits"></a><b>-digits</b> k (<i>output decimals</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The number of decimals printed when using the variance of information measure.</p>
-</div>
-</div>
-
-<a name="_section_5"></a>
-<h2>SPLIT/JOIN DISTANCE</h2>
-<p style="margin-bottom:0" class="asd_par">
-For each pair of clusterings <b>C1</b>, <b>C2</b>, two numbers are given,
-say <b>d1</b> and <b>d2</b>. Then <b>d1</b> + <b>d2</b> equals the number
-of nodes that have to be exchanged in order to transform any of the two
-clusterings into the other, and you can think of (<b>d1</b>+<b>d2</b>)/<b>2N</b>
-as the percentage that the two clusterings differ. The split/join
-distance has a linearity property with respect to the meet of <b>C1</b> and
-<b>C2</b>, see below.</p>
-<p style="margin-bottom:0" class="asd_par">
-The split/join distance <b>sjd</b> is very handy in computing the consistency of
-two or more clusterings of the same graph, or comparing clusterings made
-with different resource (but otherwise identical) parameters. The latter is
-for finding out whether you can settle for cheaper mcl settings, or whether
-you need to switch to more expensive settings. The former is for finding out
-whether clusterings are identical, conflicting, or whether one is (almost) a
-subclustering of the other - mostly for comparing a set of clusterings of
-different granularity, made by letting the mcl parameter <b>-I</b> vary.
-The <a class="intern" href="#examples">EXAMPLES</a> section contains examples of all these <b>clm dist</b> uses,
-and the use of <b>clm info</b> and <b>clm meet</b> is also discussed there.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>sjd</b> is a metric distance on the space of partitions of
-a set of a given fixed cardinality. It has the following linearity
-property. Let <b>P1</b> and <b>P2</b> be partitions, then</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>sjd</b>(<b>P1</b>, <b>P2</b>) = <b>sjd</b>(<b>P1</b>, <b>D</b>) + <b>sjd</b>(<b>P2</b>, <b>D</b>)</p>
-<p style="margin-bottom:0" class="asd_par">
-where <b>D</b> (for Dutch Doorsnede)
-is the intersection of <b>P1</b> and <b>P2</b>, i.e. the unique clustering
-that is both a subclustering of <b>P1</b> and <b>P2</b> <i>and</i> a superclustering of
-all other subclusterings of <b>P1</b> and <b>P2</b>. Sloppily worded, <b>D</b> is the largest
-subclustering of both <b>P1</b> and <b>P2</b>. See the <a class="intern" href="#references">REFERENCES</a> section for
-a pointer to the technical report in which <b>sjd</b> was first defined (and in
-which the non-trivial triangle inequality is proven).</p>
-<p style="margin-bottom:0" class="asd_par">
-Because it is useful to know whether one partition (or clustering)
-is almost a subclustering of the other, <b>clm dist</b> returns the
-two constituents <b>sjd</b>(<b>P1</b>,<b>D</b>) and <b>sjd</b>(<b>P2</b>,<b>D</b>).</p>
-<p style="margin-bottom:0" class="asd_par">
-Let <b>P1</b> and <b>P2</b> be two clusterings of a graph of cardinality <b>N</b>,
-and suppose <b>clm dist</b> returns the integers <b>d1</b> and <b>d2</b>. You can think of
-<b>100 * (d1 + d2) / N</b> as the percentage that <b>P1</b> and <b>P2</b> differ.
-This interpretation is in fact slightly conservative.
-The numerator is the number of nodes that need to be exchanged in order to
-transform one into the other. This number may grow as large as
-<b>2*N - 2*sqrt(N)</b>, so it would be justified to take 50 as a scaling
-factor rather than 100.</p>
-<p style="margin-bottom:0" class="asd_par">
-For example, if <b>A</b> and <b>B</b> are both clusterings of a graph
-on a set of 9058 nodes and <b>clm dist</b> returns [38, 2096], this conveys
-that <b>A</b> is almost a subclustering of <b>B</b> (by splitting 38 nodes
-in <b>A</b> we obtain a clustering <b>D</b> that is a subclustering of <b>B</b>),
-and that <b>B</b> is much less granular than <b>A</b>. The latter is
-because we can obtain <b>B</b> from <b>D</b> by <i>joining</i> 2096 nodes
-in some way.</p>
-
-<a name="examples"></a>
-<h2>EXAMPLES</h2>
-<p style="margin-bottom:0" class="asd_par">
-The following is an example of several mcl validation tools
-applied to a set of clusterings on a protein graph of 9058 nodes.
-In the first experiment, six
-different clusterings were generated for different values of the inflation
-parameter, which was respectively set to 1.2, 1.6, 2.0, 2.4, 2.8, and 3.2.
-It should be noted that protein graphs seem somewhat special in that an
-inflation parameter setting as low as 1.2 still produces a very acceptable
-clustering. The six clusterings are scrutinized using <b>clm dist</b>,
-<b>clm info</b>, and <b>clm meet</b>.
-In the second experiment, four different clusterings were generated
-with identical flow (i.e. inflation) parameter, but
-with different resource parameters. <b>clm dist</b> is used to choose
-a sufficient resource level.</p>
-<p style="margin-bottom:0" class="asd_par">
-High <b>-P/-S/-R</b> values make <b>mcl</b> more accurate but also
-more time and memory consuming. Run <b>mcl</b> with different settings for these
-parameters, holding other parameters fixed. If the expensive and supposedly
-more accurate clusterings are very similar to the clusterings resulting from
-cheaper settings, the cheaper setting is sufficient. If the distances
-between cheaper clusterings and more expensive clusterings are large, this
-is an indication that you need the expensive settings. In that case, you may
-want to increase the <b>-P/-S/-R</b> parameters (or simply the
-<b>-scheme</b> parameter) until associated
-clusterings at nearby resource levels are very similar.</p>
-<p style="margin-bottom:0" class="asd_par">
-In this particular example, the validation tools do not reveal that one
-clustering in particular can be chosen as 'best', because all clusterings
-seem at least acceptable. They do aid however in showing the relative
-merits of each clusterings. The most important issue in this respect is
-cluster granularity. The table below shows the output of <b>clm info</b>.</p>
-<div class="verbatim">
- Efficiency Mass frac Area frac Cl weight Mx link weight
-1.2 0.42364 0.98690 0.02616 52.06002 50.82800
-1.6 0.58297 0.95441 0.01353 55.40282 50.82800
-2.0 0.63279 0.92386 0.01171 58.09409 50.82800
-2.4 0.65532 0.90702 0.01091 59.58283 50.82800
-2.8 0.66854 0.84954 0.00940 63.19183 50.82800
-3.2 0.67674 0.82275 0.00845 66.10831 50.82800</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This data shows that there is exceptionally strong cluster structure present
-in the input graph. The 1.2 clustering captures almost all edge mass using
-only 2.5 percent of 'area'. The 3.2 clustering still captures 82 percent of
-the mass using less than 1 percent of area. We continue with looking at the
-mutual consistency of the six clusterings. Below is a table that shows all
-pairwise distances between the clusterings.</p>
-<div class="verbatim">
- | 1.6 | 2.0 | 2.4 | 2.8 | 3.2 | 3.6
------------------------------------------------------------.
-1.2 |2096,38 |2728,41 |3045,48 |3404,45 |3621,43 |3800, 42 |
------------------------------------------------------------|
-1.6 | | 797,72 |1204,76 |1638,78 |1919,70 |2167, 69 |
------------------------------------------------------------|
-2.0 | | | 477,68 | 936,78 |1235,85 |1504, 88 |
------------------------------------------------------------|
-2.4 | | | | 498,64 | 836,91 |1124,103 |
------------------------------------------------------------|
-2.8 | | | | | 384,95 | 688,119 |
------------------------------------------------------------|
-3.2 | | | | | | 350,110 |
------------------------------------------------------------.
-</div>
-<p style="margin-bottom:0" class="asd_par">
-The table shows that the different clusterings are pretty consistent with
-each other, because for two different clusterings it is generally true that
-one is almost a subclustering of the other. The interpretation for the
-distance between the 1.6 and the 3.2 clustering for example, is that by
-rearranging 43 nodes in the 3.2 clustering, we obtain a subclustering of the
-1.6 clustering. The table shows that for any pair of clusterings, at most
-119 entries need to be rearranged in order to make one a subclustering of
-the other.</p>
-<p style="margin-bottom:0" class="asd_par">
-The overall consistency becomes all the more clear by looking at the meet of
-all the clusterings:</p>
-<div class="verbatim">
-clm meet -o meet out12 out16 out20 out24 out28 out32
-clm dist meet out12 out16 out20 out24 out28 out32</div>
-<p style="margin-top:0em; margin-bottom:0em">
-results in the following distances between the respective clusterings
-and their meet.</p>
-<div class="verbatim">
- | 1.2 | 1.6 | 2.0 | 2.4 | 2.8 | 3.2 |
--------------- --------------------------------------------.
-meet| 0,3663| 0,1972| 0,1321 | 0,958 | 0,559 | 0,283 |
--------------- --------------------------------------------.</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This shows that by rearranging only 283 nodes in the 3.2 clustering,
-one obtains a subclustering of all other clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">
-In the last experiment, <b>mcl</b> was run with inflation parameter 1.4,
-for each of the four different preset pruning schemes <tt>k=1,2,3,4</tt>.
-The <b>clm dist</b> distances between the different clusterings
-are shown below.</p>
-<div class="verbatim">
- | k=2 | k=3 | k=4 |
--------------------------------.
-k=1 | 17,17 | 16,16 | 16,16 |
--------------------------------.
-k=2 | | 3,3 | 5,5 |
--------------------------------.
-k=3 | | | 4,4 |
--------------------------------.</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This example is a little boring in that the cheapest scheme seems adequate.
-If anything, the gaps between the <tt>k=1</tt> scheme and the rest are a little
-larger than the three gaps between the <tt>k=2</tt>, <tt>k=3</tt>, and <tt>k=4</tt>
-clusterings. Had all distances been much larger, then such an observation
-would be reason to choose the <tt>k=2</tt> setting.</p>
-<p style="margin-bottom:0" class="asd_par">
-Note that you need not feel uncomfortable with the clusterings
-still being different at high resource levels, if ever so slightly.
-In all likelihood, there are anyway nodes which are not in any core of
-attraction, and that are on the boundary between two or more clusterings.
-They may go one way or another, and these are the nodes which
-will go different ways even at high resource levels.
-Such nodes may be stable in clusterings obtained for lower inflation
-values (i.e. coarser clusterings), in which the different clusters
-to which they are attracted are merged.</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-Marina Meila. <i>Comparing Clusterings — An Axiomatic View</i>.
-In <i>Proceedings of the 22nd International Conference on Machine Learning</i>,
-Bonn, Germany, 2005.</p>
-<p style="margin-bottom:0" class="asd_par">
-Marina Meila. <i>Comparing Clusterings</i>,
-UW Statistics Technical Report 418.<br>
-<a class="extern" href="http://www.stat.washington.edu/www/research/reports/2002/tr418.ps">http://www.stat.washington.edu/www/research/reports/2002/tr418.ps</a></p>
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diff --git a/doc/clmformat.1 b/doc/clmformat.1
deleted file mode 100644
index e44b04b..0000000
--- a/doc/clmformat.1
+++ /dev/null
@@ -1,627 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clmformat" 1 "16 May 2014" "clmformat 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm format \- display cluster results in readable form
-
-(optionally with labels and/or cohesion and stickiness measures
-attached)\&.
-
-Unless used with the \fB-dump\fP\ \&\fIfname\fP or \fB--dump\fP option,
-\fBclm format\fP depends on the presence of the macro processor \fBzoem\fP, as
-described further below\&.
-
-The \fB-icl\fP\ \&\fIfname\fP input clustering option is always required\&. The
-\fB-imx\fP\ \&\fIfname\fP input matrix option is required in fancy mode\&. The tab
-file option \fB-tab\fP\ \&\fIfname\fP is needed if you want label information in
-the output rather than mcl identifiers\&.
-.SH SYNOPSIS
-
-\fBclm format\fP has two different modes of output: \fIdump\fP and \fIfancy\fP\&.
-If neither is specified, \fIfancy\fP is used\&. In this mode, \fBclm format\fP
-generates a large arrary of performance measures related to nodes and
-clusters in both interlinked html output and plain text files\&. The files
-will be contained in an output directory that is newly created if not yet
-existing\&. In fancy mode the \fB-imx\fP option is required and the macro
-processor \fBzoem\fP must be available (http://micans\&.org/zoem)\&.
-
-If \fIdump\fP is specified (see below how to do this) \fBclm format\fP just
-generates a dump file where each line
-contains a cluster in the form of tab-separated indices, or tab-separated
-labels in case the \fB-tab\fP option is used\&. This dump is easy to parse
-with a simple or even quick-and-dirty script\&.
-You can include some very simple performance measures in this dump file
-by supplying \fB--dump-measures\fP\&. Use
-\fB-dump\fP\ \&\fIfname\fP to specify the name of the file to dump to, rather
-than having \fBclm format\fP construct a file name by itself\&.
-
-\fBclm format\fP can combine the both modes by using either \fB--dump\fP or
-\fB-dump\fP\ \&\fIfname\fP \fIand\fP \fB--fancy\fP\&. In this case the dump file
-will be created in the output directory that is used by \fIfancy\fP mode\&.
-
-\fBclm format\fP
-
-\fB-icl\fP fname (\fIinput cluster file\fP)
-\fB-imx\fP fname (\fIinput matrix/graph file\fP)
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-pi\fP num (\fIapply pre-inflation to matrix\fP)\fB]\fP
-\fB[-tab\fP fname (\fIread tab file\fP)\fB]\fP
-\fB[--lazy-tab\fP (\fIallow mismatched tab-file\fP)\fB]\fP
-\fB[-lump-count\fP n (\fInode threshold\fP)\fB]\fP
-\fB[--dump\fP (\fIwrite dump to dump\&.<icl-name>\fP)\fB]\fP
-\fB[-dump\fP fname (\fIwrite dump to file\fP)\fB]\fP
-\fB[--dump-pairs\fP (\fIwrite cluster/node pair per line\fP)\fB]\fP
-\fB[--dump-measures\fP (\fIwrite simple performance measures\fP)\fB]\fP
-\fB[-dump-node-sep\fP str (\fIseparate entries with str\fP)\fB]\fP
-\fB[--fancy\fP (\fIspawn information blizzard\fP)\fB]\fP
-\fB[-dir\fP dirname (\fIwrite results to directory\fP)\fB]\fP
-\fB[-infix\fP str (\fIuse after base name/directory\fP)\fB]\fP
-\fB[-nsm\fP fname (\fIoutput node stickiness file\fP)\fB]\fP
-\fB[-ccm\fP fname (\fIoutput cluster cohesion file\fP)\fB]\fP
-\fB[--adapt\fP (\fIallow domain mismatch\fP)\fB]\fP
-\fB[--subgraph\fP (\fItake subgraph with --adapt\fP)\fB]\fP
-\fB[-zmm\fP fname (\fIassume macro definitions are in fname\fP)\fB]\fP
-\fB[-fmt\fP fname (\fIwrite to encoding file fname\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-
-Consult the option descriptions and the introduction above for
-interdependencies of options\&.
-
-\fBclm format\fP generates in fancy mode a logical description of the
-to-be-formatted content in a very small vocabulary of format-specific
-zoem macros\&. The appearance of the output can be easily changed by adapting
-a zoem macro definition file (also output by \fBclm format\fP) that is used by the
-zoem interpreter to interpret the logical elements\&.
-
-The output format is apt to change over subsequent releases, as a result of
-user feedback\&. Such changes will most likely be confined to the zoem macro
-definition file\&.
-
-The OUTPUT EXPLAINED section further below is likely to be of interest\&.
-.SH DESCRIPTION
-
-The primary function of \fBclm format\fP is to display cluster results and
-associated confidence measures in a readable form, by listing clusters in
-terms of the labels associated with the indices that are used in the mcl
-matrix\&. The labels must be stored in a so called \fItab\fP file; see the
-\fB-tab\fP option for more information\&.
-
-\fBNOTE\fP
-.br
-\fBclm format\fP output is in the form of \fIzoem\fP macros\&.
-You need to have zoem installed in your system if you want \fBclm format\fP
-to be of use\&. Zoem will not be necessary if you are using
-the \fB-dump\fP option\&.
-
-The \fB-imx\fP\ \&\fImx\fP option is required
-unless the \fB-dump\fP option is used\&. The latter option
-results in special behaviour described under the
-\fB-dump\fP\ \&\fIfname\fP entry\&.
-
-Output is by default written in a directory that
-is newly created if it does not yet exist (normally several files
-will be created, for which the directory acts as a natural container)\&.
-It is possible to simply output to the current directory, for that you need
-to specify \fB-dir\fP\ \&\fB\&./\fP\&. If \fB-dir\fP is not specified, the output
-directory \fCfmt\&.<clname>\fP will be used, where \fC<clname>\fP is the argument
-to the \fB-cl\fP option\&. In the output directory, \fBclm format\fP will
-normally write two files\&. One contains zoem macros encoding formatted output
-(the encoding file), and the second (the definition file) contains zoem
-macro definitions which are used by the former\&.
-
-The encoding file is by default called \fCfmt\&.azm\fP
-(cf\&. the \fB-fmt\fP\ \&\fIfname\fP option)\&.
-It contains \fIzoem\fP macros\&. It imports the macro definition file
-called \fCclmformat\&.zmm\fP
-that is normally also written by \fBclm format\fP\&. Another macro definition
-file can be specified by using the \fB-zmm\fP\ \&\fI<defsname>\fP
-option\&. In this case \fBclm format\fP will refrain from writing the definition
-file and replace mentions of \fCclmformat\&.zmm\fP in the encoding file
-by \fC<defsname>\fP\&.
-
-The encoding file needs to be processed by issuing one of the following
-commands from within the directory where the file is located\&.
-
-.di ZV
-.in 0
-.nf \fC
- zoem -i fmt -d html
- zoem -i fmt -d txt
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The first will result in HTML formatted output, the second in
-plain text format\&. Obviously, you need to have installed zoem
-(e\&.g\&. from http://micans\&.org/zoem/src/) for this to work\&.
-
-For each cluster a paragraph is output\&. First comes a listing of other
-clusters (in order of relevance, possibly empty) for which a significant
-amount of edges exists between the other and the current cluster\&. Second
-comes a listing of the nodes in the current cluster\&. For each node a small
-sublist is made (in order of relevance, possibly empty) of other clusters in
-which the node has neighbours and for which the total sum of corresponding
-edge weights is significant\&.
-Several quantities are output for each node/cluster pair that is
-deemed relevant\&. These are explained in the section OUTPUT EXPLAINED\&.
-
-Clusters will by default be output to file until the total node count has
-exceeded a threshold (refer to the \fB-lump-count\fP
-option)\&.
-
-\fBclm format\fP also shows how well each node fits in the cluster it is in and
-how cohesive each cluster is, using simple but effective measures
-(described in section OUTPUT EXPLAINED)\&.
-This enables you to compare the quality of the clusters in a clustering
-relative to each other, and may help in identifying both interesting areas
-and areas for which cluster structure is hard to find or perhaps absent\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-icl\fP fname (\fIinput cluster file\fP)"
-\&
-.br
-Name of the clustering file\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP fname (\fIinput matrix/graph file\fP)"
-\&
-.br
-Name of the graph/matrix file\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP spec (\fIapply tf-spec to input matrix\fP)"
-\&
-.br
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP fname (\fIread tab file\fP)"
-\&
-.br
-The file \fCfname\fP should be in \fItab format\fP\&. Refer
-to \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB--lazy-tab\fP (\fIallow mismatched tab-file\fP)"
-\&
-.br
-Allow missing and spurious entries in the tab file\&.
-.in -2m
-
-.ZI 2m "\fB-dump\fP fname (\fIwrite dump to file\fP)"
-\&
-.br
-Clusters are written to file\&. For each cluster a single line is written
-containing all indices of all nodes in that cluster\&. The indices are
-separated by tabs\&. If a tab file is specified, the indices are replaced by
-the corresponding tab file entry\&.
-.in -2m
-
-.ZI 2m "\fB--dump\fP (\fIwrite dump to file\fP)"
-\&
-.br
-As \fB-dump\fP\ \&\fIfname\fP except that \fBclm format\fP writes to the file
-named \fCdump\&.<icl-name>\fP where \fC<icl-name>\fP is the argument to
-the \fB-icl\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-infix\fP str (\fIincorporate in base name\fP)"
-\&
-.br
-\fIstr\fP is included in the output file names\&.
-This can be used to store the results of different \fBclm format\fP runs
-(e\&.g\&. with differing \fB-tf\fP arguments) in the same directory\&.
-.in -2m
-
-.ZI 2m "\fB--fancy\fP (\fIforce fancy mode\fP)"
-\&
-.br
-This enforces fancy mode if either of \fB-dump\fP or \fB--dump\fP
-is given\&. The dump file will be created in the output directory\&.
-.in -2m
-
-.ZI 2m "\fB--dump-pairs\fP (\fIwrite cluster/node pair per line\fP)"
-\&
-.br
-Rather than writing a single cluster on each line, write a single
-cluster index/node (either tab entry or index) pair per line\&.
-Works in conjunction with the
-\fB-tab\fP and \fB-imx\fP options\&.
-.in -2m
-
-.ZI 2m "\fB--dump-measures\fP (\fIwrite simple performance measures\fP)"
-\&
-.br
-If an input matrix is specified with \fB-imx\fP\ \&\fIfname\fP, three
-measures of efficiency are prepended, respectively the simple projection
-score, efficiency or coverage, and the max-efficiency or max-coverage\&.
-.in -2m
-
-.ZI 2m "\fB-dump-node-sep\fP str (\fIseparate entries with str\fP)"
-\&
-.br
-Separate entries in the dump file with \fBstr\fP\&.
-.in -2m
-
-.ZI 2m "\fB-pi\fP num (\fIapply pre-inflation to matrix\fP)"
-\&
-.br
-Apply pre-inflation to the matrix specified with the \fB-imx\fP option\&.
-This will cause the efficiency scores to place a higher reward on
-high-weight edges being covered by a clustering (assuming that
-\fInum\fP is larger than one)\&.
-
-This option is also useful when \fBmcl\fP itself was instructed to use
-pre-inflation when clustering a graph\&.
-.in -2m
-
-.ZI 2m "\fB-lump-count\fP n (\fInode threshold\fP)"
-\&
-.br
-The zoem file is created such that during zoem processing clusters are
-formatted and output within a single file until the node threshold has been
-exceeded\&. A new file is then opened and the procedure repeats itself\&.
-.in -2m
-
-.ZI 2m "\fB--adapt\fP (\fIallow domain mismatch\fP)"
-\&
-.br
-Allow the cluster domain to differ from the graph domain\&. Presumably
-the clustering is a clustering of a subgraph\&. The cohesion and stickiness
-measures will pertain to the relevant part of the graph only\&.
-.in -2m
-
-.ZI 2m "\fB--subgraph\fP (\fIuse restriction\fP)"
-\&
-.br
-If the cluster domain is a subset of the graph domain, the cohesion and
-stickiness measures will by default still pertain to the entire graph\&. By
-setting this option, the measures will pertain to the subgraph induced by
-the cluster domain\&.
-.in -2m
-
-.ZI 2m "\fB-dir\fP dirname (\fIwrite results to directory\fP)"
-\&
-.br
-Use \fBdirname\fP as output directory\&. It will be created
-if it does not exist already\&.
-.in -2m
-
-.ZI 2m "\fB-fmt\fP fname (\fIwrite to encoding file fname\fP)"
-\&
-.br
-Write to encoding file \fBfname\fP rather than the default \fCfmt\&.azm\fP\&.
-It is best to supply fname with the standard zoem suffix \fC\&.azm\fP\&. Zoem
-will process file of any name, but those lacking the \fC\&.azm\fP suffix must be
-specified using the zoem \fB-I\fP\ \&\fIfname\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-zmm\fP defsname (\fIassume macro definitions are in fname\fP)"
-\&
-.br
-If this option is used, \fBclm format\fP will not output the definition file,
-and mentions of the definition file in the encoding file will use
-the file name \fCdefsname\fP\&. This option assumes that a valid definition
-file by the name of \fCdefsname\fP does exist\&.
-.in -2m
-
-.ZI 2m "\fB-nsm\fP fname (\fIoutput node stickiness file\fP)"
-\&
-.br
-This option specifies the name in which to store (optionally) the \fBnode
-stickiness matrix\fP\&. It has the following structure\&. The columns range over
-all elements in the graph as specified by the \fB-imx\fP option\&.
-The rows range over the clusters as specified by the \fB-icl\fP option\&.
-The entries contain the projection value of that particular
-node onto that particular clusters, i\&.e\&. the sum of the weights of
-all arcs going out from the node to some node in that cluster, written
-as a fraction relative to the sum of weights of all outgoing arcs\&.
-.in -2m
-
-.ZI 2m "\fB-ccm\fP fname (\fIoutput cluster cohesion file\fP)"
-\&
-.br
-This option specifies the name of the file in which to store (optionally)
-the \fBcluster cohesion matrix\fP\&. It has the following structure\&.
-Both columns and rows range over all clusters in the clustering as specified
-by the \fB-icl\fP option\&. An entry specifies the projection
-of one cluster onto another cluster, which is simply the average
-of the projection value onto the second cluster of all nodes in the
-first cluster\&.
-.in -2m
-.SH OUTPUT EXPLAINED
-
-What follows is an explanation of the output provided by the
-standard zoem macros\&. The output comes in a pretty terse number-packed
-format\&. The decision was made not to include headers and captions
-in the output in order to keep it readable\&.
-You might want to print out the following annotated examples\&.
-At the same side of the equation, the following is probably tough
-reading unless you have an actual example of clmformatted output at hand\&.
-
-If you are reading this in a terminal, you might need to resize
-it to have width larger than 80 columns, as the examples below
-are formatted in verbatim mode\&.
-
-Below mention is made of the projection value for a node/cluster pair\&.
-This is simply the total amount of edge weights for that node
-in that cluster (corresponding to neighbours of the node in the
-cluster) relative to the overall amount of edge weights for that node
-(corresponding to all its neighbours)\&.
-The coverage measure (refered to as \fBcov\fP)
-is also used\&. This is similar to the projection
-value, except that a) the coverage measure rewards the inclusion
-of large edge weights (and penalizes the inclusion of insignificant
-edge weights) and b) rewards node/cluster pairs for which the neighbour set
-of the node is very similar to the cluster\&.
-The maximum coverage measure (refered to as \fBmaxcov\fP) is similar
-to the normal coverage measure except that it rewards inclusion
-of large edge weights even more\&.
-The cov and maxcov performance measures have several nice continuity and
-monotonicity properties and are described in [1]\&.
-
-\fBExample cluster header\fP
-.br
-
-.di ZV
-.in 0
-.nf \fC
-Cluster 0 sz 15 self 0\&.82 cov 0\&.43-0\&.26
- 10: 0\&.11
- 18: 0\&.05
- 12: 0\&.02
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBexplanation\fP
-.br
-
-.di ZV
-.in 0
-.nf \fC
-Cluster 0 sz 15 self 0\&.82 cov 0\&.43-0\&.26
- | | | | |
- clid count proj cov covmax
-
- 10: 0\&.11
- | |
-clidx1 projx1
-
- 18: 0\&.05
- | |
-clidx2 projx2
-
-clid Numeric cluster identifier (arbitrarily) assigned by MCL\&.
-count The size of cluster clid\&.
-proj Projection value for cluster clid [d]\&.
-cov Coverage measure for cluster clid [d]\&.
-maxcov Max-coverage measure for cluster clid [d]\&.
-clidx1 Index of other cluster sharing relatively many edges\&.
-projx1 Projection value for the clid/clidx1 pair of clusters [e]\&.
-clidx2 :
-projx2 : as clidx1 and projx1
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBExample inner node\fP
-.br
-An inner node is listed under a cluster, and it is simply a member of that
-cluster\&. The name is as opposed to \&'outer node\&', described below\&.
-
-.di ZV
-.in 0
-.nf \fC
-[foo bar zut]
- 21 7-5 0\&.73 0\&.420-0\&.331 0\&.282-0\&.047 0\&.071-0\&.035 <3\&.54>
- 10 6/3 0\&.16 0\&.071-0\&.047 0\&.268-0\&.442
- 12 4/2 0\&.11 0\&.071-0\&.035 0\&.296-0\&.515
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBexplanation\fP
-.br
-
-.di ZV
-.in 0
-.nf \fC
-[label]
- 21 7-5 0\&.73 0\&.420-0\&.331 0\&.282-0\&.047 0\&.071-0\&.035 <3\&.54>
- | | | | | | | | | | |
- idx nbi nbo proj cov covmax max_i min_i max_o-min_o SUM
-
- 10 6/3 0\&.16 0\&.268-0\&.442 0\&.071-0\&.047
- | | | | | | | |
- clusid sz nb proj cov covmax max_i min_i
-
-label Optional; with -tab <tabfile> option\&.
-idx Numeric (mcl) identifier\&.
-nbi Count of the neighbours of node idx within its cluster\&.
-nbo Count of the neighbours of node idx outside its cluster\&.
-proj Projection value [a] of nbi edges\&.
-cov Skewed projection [b], rewards inclusion of large edge weights\&.
-covmax As cov above, rewarding large edge weights even more\&.
-max_i Largest edge weight in the nbi set, normalized [c]\&.
-min_i Smallest edge weight in the nbi set [c]\&.
-max_o Largest edge weight outside the nbi set [c]
-min_o Smallest edge weight outside the nbi set [c]\&.
-SUM The sum of all edges leaving node idx\&.
-
-clusid Index of other cluster that is relevant for node idx\&.
-sz Size of that cluster\&.
-nb Count of neighbours of node idx in cluster clusid\&.
-proj Projection value of edges from node idx to cluster clusid\&.
-cov Skewed projection of edges from node idx to cluster clusid\&.
-covmax Maximally skewed projection, as above\&.
-max_o Largest edge weight for node idx to cluster clusid [c]\&.
-min_o Smallest edge weight for node idx to cluster clusid [c]\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBExample outer node\fP
-.br
-An outer node is listed under a cluster\&. The node is not part of that
-cluster, but seems to have substantial connections to that cluster\&.
-
-.di ZV
-.in 0
-.nf \fC
-[zoo eek few]
- 29 18#2 2-5 0\&.65 0\&.883-0\&.815 0\&.436-0\&.218 0\&.073-0\&.055
- /4 0\&.27 0\&.070-0\&.109 0\&.073-0\&.055
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBexplanation\fP
-.br
-
-.di ZV
-.in 0
-.nf \fC
-[label]
- 29 18#2 2-5 0\&.65 0\&.883-0\&.815 0\&.436-0\&.218 0\&.073-0\&.055
- | | | | | | | | | | | |
- idx cl sz nbi nbo proj cov maxcov max_i min_i max_o min_o
- id
- /4 0\&.27 0\&.070-0\&.109 0\&.073-0\&.055 <2\&.29>
- | | | | | | |
- nb proj cov maxcov max_i min_i SUM
-
-label Optional; with -tab <tabfile> option\&.
-idx Numeric (mcl) identifier
-clid Index of the cluster that node idx belongs to
-sz Size of the cluster that node idx belongs to
-proj :
-cov : All these entries are the same as described above
-covmax : for inner nodes, pertaining to cluster clid,
-max_i : i\&.e\&. the native cluster for node idx
-min_i : (it is a member of that cluster)\&.
-max_o :
-min_o :
-
-nb The count of neighbours of node idx in the current cluster
-proj Projection value for node idx relative to current cluster\&.
-cov Skewed projection (rewards large edge weights), as above\&.
-covmax Maximally skewed projection, as above\&.
-max_o Largest edge weight for node idx in current cluster [c]\&.
-min_o smallest edge weight for node idx in current cluster [c]\&.
-SUM The sum of *all* edges leaving node idx\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.ZJ 1m 2m "[a]"
-The projection value for a node relative to some subset of
-its neighbours is the sum of edge weights of all edges to that
-subset\&. The sum is witten as a fraction relative to the sum
-of edge weights of all neighbours\&.
-.in -3m
-
-.ZJ 1m 2m "[b]"
-cov and covmax stand for coverage and maximal coverage\&.
-The coverage measure of a node/cluster pair is a generalized and skewed
-projection value [a] that rewards the presence of large edge weights in the
-cluster, relative to the collection of weights of all edges departing from
-the node\&. The maxcov measure is a projection value skewed even further,
-correspondingly rewarding the inclusion of large edge weights\&. The cov and
-maxcov performance measures have several nice continuity properties and are
-described in [1]\&.
-.in -3m
-
-.ZJ 1m 2m "[c]"
-All edge weights are written as the fraction of the sum
-SUM of all edge weights of edges leaving node idx\&.
-.in -3m
-
-.ZJ 1m 2m "[d]"
-For clusters the projection value and the coverage measures
-are simply the averages of all projection values [a], respectively
-coverage measures [b], taken over all nodes in the cluster\&.
-The cluster projection value simply measures the sum of edge
-weights internal to the cluster, relative to the total sum of
-edge weights of all edges where at least one node in the edge
-is part of the cluster\&.
-.in -3m
-
-.ZJ 1m 2m "[e]"
-The projection value for start cluster x and end cluster y
-is the sum of edge weights of edges between x and y as a fraction
-of the sum of all edge weights of edges leaving x\&.
-.in -3m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH REFERENCES
-
-[1]
-Stijn van Dongen\&. \fIPerformance criteria for graph clustering and Markov
-cluster experiments\fP\&. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0012\&.ps\&.Z
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmformat.html b/doc/clmformat.html
deleted file mode 100644
index 57c0448..0000000
--- a/doc/clmformat.html
+++ /dev/null
@@ -1,674 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
-margin-right: 0%;
-}
-a:link { text-decoration: none; }
-a:active { text-decoration: none; }
-a:visited { text-decoration: none; }
-a:link { color: #1111aa; }
-a:active { color: #1111aa; }
-a:visited { color: #111166; }
-a.local:link { color: #11aa11; }
-a.local:active { color: #11aa11; }
-a.local:visited { color: #116611; }
-a.intern:link { color: #1111aa; }
-a.intern:active { color: #1111aa; }
-a.intern:visited { color: #111166; }
-a.extern:link { color: #aa1111; }
-a.extern:active { color: #aa1111; }
-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
-}
-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
-.item_leftalign { text-align: left; }
-.item_rightalign
-{ width: 2em;
-text-align: right;
-}
-.item_compact .item_rightalign
-{ position: absolute;
-width: 52em;
-right: -2em;
-text-align: right;
-}
-.item_text
-{ position: relative;
-margin-left: 3em;
-}
-.smallcaps { font-size: smaller; text-transform: uppercase }
-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
-margin-right: 8%;
-}
-</style>
-<title>The clmformat manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmformat.ps"><b>clmformat</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#xpl">OUTPUT EXPLAINED</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm format — display cluster results in readable form</p>
-<p style="margin-bottom:0" class="asd_par">
-(optionally with labels and/or cohesion and stickiness measures
-attached).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Unless used with the <b>-dump</b> <i>fname</i> or <b>--dump</b> option,
-<b>clm format</b> depends on the presence of the macro processor <b>zoem</b>, as
-described further below.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-icl</b> <i>fname</i> input clustering option is always required. The
-<b>-imx</b> <i>fname</i> input matrix option is required in fancy mode. The tab
-file option <b>-tab</b> <i>fname</i> is needed if you want label information in
-the output rather than mcl identifiers.
-</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm format</b> has two different modes of output: <i>dump</i> and <i>fancy</i>.
-If neither is specified, <i>fancy</i> is used. In this mode, <b>clm format</b>
-generates a large arrary of performance measures related to nodes and
-clusters in both interlinked html output and plain text files. The files
-will be contained in an output directory that is newly created if not yet
-existing. In fancy mode the <b>-imx</b> option is required and the macro
-processor <b>zoem</b> must be available (<a class="extern" href="http://micans.org/zoem">http://micans.org/zoem</a>).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If <i>dump</i> is specified (see below how to do this) <b>clm format</b> just
-generates a dump file where each line
-contains a cluster in the form of tab-separated indices, or tab-separated
-labels in case the <b>-tab</b> option is used. This dump is easy to parse
-with a simple or even quick-and-dirty script.
-You can include some very simple performance measures in this dump file
-by supplying <b>--dump-measures</b>. Use
-<b>-dump</b> <i>fname</i> to specify the name of the file to dump to, rather
-than having <b>clm format</b> construct a file name by itself.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm format</b> can combine the both modes by using either <b>--dump</b> or
-<b>-dump</b> <i>fname</i> <i>and</i> <b>--fancy</b>. In this case the dump file
-will be created in the output directory that is used by <i>fancy</i> mode.
-</p>
-<p style="margin-bottom:0" class="asd_par"><b>clm format</b></p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#opt-icl"><b>-icl</b> fname (<i>input cluster file</i>)</a>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input matrix/graph file</i>)</a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-pi"><b>[-pi</b> num (<i>apply pre-inflation to matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> fname (<i>read tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt--lazy-tab"><b>[--lazy-tab</b> (<i>allow mismatched tab-file</i>)<b>]</b></a>
-<a class="intern" href="#opt-lump-count"><b>[-lump-count</b> n (<i>node threshold</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump"><b>[--dump</b> (<i>write dump to dump.<icl-name></i>)<b>]</b></a>
-<a class="intern" href="#opt-dump"><b>[-dump</b> fname (<i>write dump to file</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-pairs"><b>[--dump-pairs</b> (<i>write cluster/node pair per line</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-measures"><b>[--dump-measures</b> (<i>write simple performance measures</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump-node-sep"><b>[-dump-node-sep</b> str (<i>separate entries with str</i>)<b>]</b></a>
-<a class="intern" href="#opt--fancy"><b>[--fancy</b> (<i>spawn information blizzard</i>)<b>]</b></a>
-<a class="intern" href="#opt-dir"><b>[-dir</b> dirname (<i>write results to directory</i>)<b>]</b></a>
-<a class="intern" href="#opt-infix"><b>[-infix</b> str (<i>use after base name/directory</i>)<b>]</b></a>
-<a class="intern" href="#opt-nsm"><b>[-nsm</b> fname (<i>output node stickiness file</i>)<b>]</b></a>
-<a class="intern" href="#opt-ccm"><b>[-ccm</b> fname (<i>output cluster cohesion file</i>)<b>]</b></a>
-<a class="intern" href="#opt--adapt"><b>[--adapt</b> (<i>allow domain mismatch</i>)<b>]</b></a>
-<a class="intern" href="#opt--subgraph"><b>[--subgraph</b> (<i>take subgraph with --adapt</i>)<b>]</b></a>
-<a class="intern" href="#opt-zmm"><b>[-zmm</b> fname (<i>assume macro definitions are in fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-fmt"><b>[-fmt</b> fname (<i>write to encoding file fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0" class="asd_par">Consult the option descriptions and the introduction above for
-interdependencies of options.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm format</b> generates in fancy mode a logical description of the
-to-be-formatted content in a very small vocabulary of format-specific
-zoem macros. The appearance of the output can be easily changed by adapting
-a zoem macro definition file (also output by <b>clm format</b>) that is used by the
-zoem interpreter to interpret the logical elements.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The output format is apt to change over subsequent releases, as a result of
-user feedback. Such changes will most likely be confined to the zoem macro
-definition file.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The OUTPUT EXPLAINED section further below is likely to be of interest.
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The primary function of <b>clm format</b> is to display cluster results and
-associated confidence measures in a readable form, by listing clusters in
-terms of the labels associated with the indices that are used in the mcl
-matrix. The labels must be stored in a so called <i>tab</i> file; see the
-<a class="intern" href="#opt-tab"><b>-tab</b></a> option for more information.
-</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-<b>clm format</b> output is in the form of <i>zoem</i> macros.
-You need to have zoem installed in your system if you want <b>clm format</b>
-to be of use. Zoem will not be necessary if you are using
-the <b>-dump</b> option.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <a class="intern" href="#opt-imx"><b>-imx</b> <i>mx</i></a> option is required
-unless the <b>-dump</b> option is used. The latter option
-results in special behaviour described under the
-<a class="intern" href="#opt-dump"><b>-dump</b> <i>fname</i></a> entry.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Output is by default written in a directory that
-is newly created if it does not yet exist (normally several files
-will be created, for which the directory acts as a natural container).
-It is possible to simply output to the current directory, for that you need
-to specify <b>-dir</b> <b>./</b>. If <b>-dir</b> is not specified, the output
-directory <tt>fmt.<clname></tt> will be used, where <tt><clname></tt> is the argument
-to the <b>-cl</b> option. In the output directory, <b>clm format</b> will
-normally write two files. One contains zoem macros encoding formatted output
-(the encoding file), and the second (the definition file) contains zoem
-macro definitions which are used by the former.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The encoding file is by default called <tt>fmt.azm</tt>
-(cf. the <a class="intern" href="#opt-fmt"><b>-fmt</b> <i>fname</i></a> option).
-It contains <i>zoem</i> macros. It imports the macro definition file
-called <tt>clmformat.zmm</tt>
-that is normally also written by <b>clm format</b>. Another macro definition
-file can be specified by using the <a class="intern" href="#opt-zmm"><b>-zmm</b> <i><defsname></i></a>
-option. In this case <b>clm format</b> will refrain from writing the definition
-file and replace mentions of <tt>clmformat.zmm</tt> in the encoding file
-by <tt><defsname></tt>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The encoding file needs to be processed by issuing one of the following
-commands from within the directory where the file is located.
-</p>
-<div class="verbatim"> zoem -i fmt -d html
- zoem -i fmt -d txt</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The first will result in HTML formatted output, the second in
-plain text format. Obviously, you need to have installed zoem
-(e.g. from <a class="extern" href="http://micans.org/zoem/src/">http://micans.org/zoem/src/</a>) for this to work.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For each cluster a paragraph is output. First comes a listing of other
-clusters (in order of relevance, possibly empty) for which a significant
-amount of edges exists between the other and the current cluster. Second
-comes a listing of the nodes in the current cluster. For each node a small
-sublist is made (in order of relevance, possibly empty) of other clusters in
-which the node has neighbours and for which the total sum of corresponding
-edge weights is significant.
-Several quantities are output for each node/cluster pair that is
-deemed relevant. These are explained in the section OUTPUT EXPLAINED.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Clusters will by default be output to file until the total node count has
-exceeded a threshold (refer to the <a class="intern" href="#opt-lump-count"><b>-lump-count</b>
-option</a>).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm format</b> also shows how well each node fits in the cluster it is in and
-how cohesive each cluster is, using simple but effective measures
-(described in section OUTPUT EXPLAINED).
-This enables you to compare the quality of the clusters in a clustering
-relative to each other, and may help in identifying both interesting areas
-and areas for which cluster structure is hard to find or perhaps absent.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> fname (<i>input cluster file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Name of the clustering file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input matrix/graph file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Name of the graph/matrix file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> spec (<i>apply tf-spec to input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> fname (<i>read tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file <tt>fname</tt> should be in <i>tab format</i>. Refer
-to <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--lazy-tab"></a><b>--lazy-tab</b> (<i>allow mismatched tab-file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Allow missing and spurious entries in the tab file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dump"></a><b>-dump</b> fname (<i>write dump to file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Clusters are written to file. For each cluster a single line is written
-containing all indices of all nodes in that cluster. The indices are
-separated by tabs. If a tab file is specified, the indices are replaced by
-the corresponding tab file entry.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--dump"></a><b>--dump</b> (<i>write dump to file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-As <b>-dump</b> <i>fname</i> except that <b>clm format</b> writes to the file
-named <tt>dump.<icl-name></tt> where <tt><icl-name></tt> is the argument to
-the <b>-icl</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-infix"></a><b>-infix</b> str (<i>incorporate in base name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<i>str</i> is included in the output file names.
-This can be used to store the results of different <b>clm format</b> runs
-(e.g. with differing <b>-tf</b> arguments) in the same directory.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fancy"></a><b>--fancy</b> (<i>force fancy mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This enforces fancy mode if either of <b>-dump</b> or <b>--dump</b>
-is given. The dump file will be created in the output directory.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--dump-pairs"></a><b>--dump-pairs</b> (<i>write cluster/node pair per line</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Rather than writing a single cluster on each line, write a single
-cluster index/node (either tab entry or index) pair per line.
-Works in conjunction with the
-<a class="intern" href="#opt-tab"><b>-tab</b></a> and <a class="intern" href="#opt-imx"><b>-imx</b></a> options.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--dump-measures"></a><b>--dump-measures</b> (<i>write simple performance measures</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If an input matrix is specified with <b>-imx</b> <i>fname</i>, three
-measures of efficiency are prepended, respectively the simple projection
-score, efficiency or coverage, and the max-efficiency or max-coverage.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dump-node-sep"></a><b>-dump-node-sep</b> str (<i>separate entries with str</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Separate entries in the dump file with <b>str</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-pi"></a><b>-pi</b> num (<i>apply pre-inflation to matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Apply pre-inflation to the matrix specified with the <b>-imx</b> option.
-This will cause the efficiency scores to place a higher reward on
-high-weight edges being covered by a clustering (assuming that
-<i>num</i> is larger than one).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This option is also useful when <b>mcl</b> itself was instructed to use
-pre-inflation when clustering a graph.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-lump-count"></a><b>-lump-count</b> n (<i>node threshold</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The zoem file is created such that during zoem processing clusters are
-formatted and output within a single file until the node threshold has been
-exceeded. A new file is then opened and the procedure repeats itself.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--adapt"></a><b>--adapt</b> (<i>allow domain mismatch</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Allow the cluster domain to differ from the graph domain. Presumably
-the clustering is a clustering of a subgraph. The cohesion and stickiness
-measures will pertain to the relevant part of the graph only.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--subgraph"></a><b>--subgraph</b> (<i>use restriction</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If the cluster domain is a subset of the graph domain, the cohesion and
-stickiness measures will by default still pertain to the entire graph. By
-setting this option, the measures will pertain to the subgraph induced by
-the cluster domain.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dir"></a><b>-dir</b> dirname (<i>write results to directory</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use <b>dirname</b> as output directory. It will be created
-if it does not exist already.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-fmt"></a><b>-fmt</b> fname (<i>write to encoding file fname</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write to encoding file <b>fname</b> rather than the default <tt>fmt.azm</tt>.
-It is best to supply fname with the standard zoem suffix <tt>.azm</tt>. Zoem
-will process file of any name, but those lacking the <tt>.azm</tt> suffix must be
-specified using the zoem <b>-I</b> <i>fname</i> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-zmm"></a><b>-zmm</b> defsname (<i>assume macro definitions are in fname</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If this option is used, <b>clm format</b> will not output the definition file,
-and mentions of the definition file in the encoding file will use
-the file name <tt>defsname</tt>. This option assumes that a valid definition
-file by the name of <tt>defsname</tt> does exist.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-nsm"></a><b>-nsm</b> fname (<i>output node stickiness file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option specifies the name in which to store (optionally) the <b>node
-stickiness matrix</b>. It has the following structure. The columns range over
-all elements in the graph as specified by the <b>-imx</b> option.
-The rows range over the clusters as specified by the <b>-icl</b> option.
-The entries contain the projection value of that particular
-node onto that particular clusters, i.e. the sum of the weights of
-all arcs going out from the node to some node in that cluster, written
-as a fraction relative to the sum of weights of all outgoing arcs.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-ccm"></a><b>-ccm</b> fname (<i>output cluster cohesion file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option specifies the name of the file in which to store (optionally)
-the <b>cluster cohesion matrix</b>. It has the following structure.
-Both columns and rows range over all clusters in the clustering as specified
-by the <b>-icl</b> option. An entry specifies the projection
-of one cluster onto another cluster, which is simply the average
-of the projection value onto the second cluster of all nodes in the
-first cluster.
-</p>
-</div>
-</div>
-
-<a name="xpl"></a>
-<h2>OUTPUT EXPLAINED</h2>
-<p style="margin-bottom:0" class="asd_par">
-What follows is an explanation of the output provided by the
-standard zoem macros. The output comes in a pretty terse number-packed
-format. The decision was made not to include headers and captions
-in the output in order to keep it readable.
-You might want to print out the following annotated examples.
-At the same side of the equation, the following is probably tough
-reading unless you have an actual example of clmformatted output at hand.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Below mention is made of the projection value for a node/cluster pair.
-This is simply the total amount of edge weights for that node
-in that cluster (corresponding to neighbours of the node in the
-cluster) relative to the overall amount of edge weights for that node
-(corresponding to all its neighbours).
-The coverage measure (refered to as <b>cov</b>)
-is also used. This is similar to the projection
-value, except that a) the coverage measure rewards the inclusion
-of large edge weights (and penalizes the inclusion of insignificant
-edge weights) and b) rewards node/cluster pairs for which the neighbour set
-of the node is very similar to the cluster.
-The maximum coverage measure (refered to as <b>maxcov</b>) is similar
-to the normal coverage measure except that it rewards inclusion
-of large edge weights even more.
-The cov and maxcov performance measures have several nice continuity and
-monotonicity properties and are described in <a class="intern" href="#pcfgcmce">[1]</a>.
-</p>
-<p style="margin-bottom:0"><b>Example cluster header</b><br></p>
-<div class="verbatim">Cluster 0 sz 15 self 0.82 cov 0.43-0.26
- 10: 0.11
- 18: 0.05
- 12: 0.02</div>
-<p style="margin-bottom:0"><b>explanation</b><br></p>
-<div class="verbatim">Cluster 0 sz 15 self 0.82 cov 0.43-0.26
- | | | | |
- clid count proj cov covmax
-
- 10: 0.11
- | |
-clidx1 projx1
-
- 18: 0.05
- | |
-clidx2 projx2
-
-clid Numeric cluster identifier (arbitrarily) assigned by MCL.
-count The size of cluster clid.
-proj Projection value for cluster clid [d].
-cov Coverage measure for cluster clid [d].
-maxcov Max-coverage measure for cluster clid [d].
-clidx1 Index of other cluster sharing relatively many edges.
-projx1 Projection value for the clid/clidx1 pair of clusters [e].
-clidx2 :
-projx2 : as clidx1 and projx1</div>
-<p style="margin-bottom:0"><b>Example inner node</b><br>
-An inner node is listed under a cluster, and it is simply a member of that
-cluster. The name is as opposed to 'outer node', described below.
-</p>
-<div class="verbatim">[foo bar zut]
- 21 7-5 0.73 0.420-0.331 0.282-0.047 0.071-0.035 <3.54>
- 10 6/3 0.16 0.071-0.047 0.268-0.442
- 12 4/2 0.11 0.071-0.035 0.296-0.515</div>
-<p style="margin-bottom:0"><b>explanation</b><br></p>
-<div class="verbatim">[label]
- 21 7-5 0.73 0.420-0.331 0.282-0.047 0.071-0.035 <3.54>
- | | | | | | | | | | |
- idx nbi nbo proj cov covmax max_i min_i max_o-min_o SUM
-
- 10 6/3 0.16 0.268-0.442 0.071-0.047
- | | | | | | | |
- clusid sz nb proj cov covmax max_i min_i
-
-label Optional; with -tab <tabfile> option.
-idx Numeric (mcl) identifier.
-nbi Count of the neighbours of node idx within its cluster.
-nbo Count of the neighbours of node idx outside its cluster.
-proj Projection value [a] of nbi edges.
-cov Skewed projection [b], rewards inclusion of large edge weights.
-covmax As cov above, rewarding large edge weights even more.
-max_i Largest edge weight in the nbi set, normalized [c].
-min_i Smallest edge weight in the nbi set [c].
-max_o Largest edge weight outside the nbi set [c]
-min_o Smallest edge weight outside the nbi set [c].
-SUM The sum of all edges leaving node idx.
-
-clusid Index of other cluster that is relevant for node idx.
-sz Size of that cluster.
-nb Count of neighbours of node idx in cluster clusid.
-proj Projection value of edges from node idx to cluster clusid.
-cov Skewed projection of edges from node idx to cluster clusid.
-covmax Maximally skewed projection, as above.
-max_o Largest edge weight for node idx to cluster clusid [c].
-min_o Smallest edge weight for node idx to cluster clusid [c].</div>
-<p style="margin-bottom:0"><b>Example outer node</b><br>
-An outer node is listed under a cluster. The node is not part of that
-cluster, but seems to have substantial connections to that cluster.
-</p>
-<div class="verbatim">[zoo eek few]
- 29 18#2 2-5 0.65 0.883-0.815 0.436-0.218 0.073-0.055
- /4 0.27 0.070-0.109 0.073-0.055</div>
-<p style="margin-bottom:0"><b>explanation</b><br></p>
-<div class="verbatim">[label]
- 29 18#2 2-5 0.65 0.883-0.815 0.436-0.218 0.073-0.055
- | | | | | | | | | | | |
- idx cl sz nbi nbo proj cov maxcov max_i min_i max_o min_o
- id
- /4 0.27 0.070-0.109 0.073-0.055 <2.29>
- | | | | | | |
- nb proj cov maxcov max_i min_i SUM
-
-label Optional; with -tab <tabfile> option.
-idx Numeric (mcl) identifier
-clid Index of the cluster that node idx belongs to
-sz Size of the cluster that node idx belongs to
-proj :
-cov : All these entries are the same as described above
-covmax : for inner nodes, pertaining to cluster clid,
-max_i : i.e. the native cluster for node idx
-min_i : (it is a member of that cluster).
-max_o :
-min_o :
-
-nb The count of neighbours of node idx in the current cluster
-proj Projection value for node idx relative to current cluster.
-cov Skewed projection (rewards large edge weights), as above.
-covmax Maximally skewed projection, as above.
-max_o Largest edge weight for node idx in current cluster [c].
-min_o smallest edge weight for node idx in current cluster [c].
-SUM The sum of *all* edges leaving node idx.</div>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">[a]</div></div>
-<div class=" item_text " style="margin-left:3em">
-<p style="margin-top:0em; margin-bottom:0em">
-The projection value for a node relative to some subset of
-its neighbours is the sum of edge weights of all edges to that
-subset. The sum is witten as a fraction relative to the sum
-of edge weights of all neighbours.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">[b]</div></div>
-<div class=" item_text " style="margin-left:3em">
-<p style="margin-top:0em; margin-bottom:0em">
-cov and covmax stand for coverage and maximal coverage.
-The coverage measure of a node/cluster pair is a generalized and skewed
-projection value [a] that rewards the presence of large edge weights in the
-cluster, relative to the collection of weights of all edges departing from
-the node. The maxcov measure is a projection value skewed even further,
-correspondingly rewarding the inclusion of large edge weights. The cov and
-maxcov performance measures have several nice continuity properties and are
-described in <a class="intern" href="#pcfgcmce">[1]</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">[c]</div></div>
-<div class=" item_text " style="margin-left:3em">
-<p style="margin-top:0em; margin-bottom:0em">
-All edge weights are written as the fraction of the sum
-SUM of all edge weights of edges leaving node idx.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">[d]</div></div>
-<div class=" item_text " style="margin-left:3em">
-<p style="margin-top:0em; margin-bottom:0em">
-For clusters the projection value and the coverage measures
-are simply the averages of all projection values [a], respectively
-coverage measures [b], taken over all nodes in the cluster.
-The cluster projection value simply measures the sum of edge
-weights internal to the cluster, relative to the total sum of
-edge weights of all edges where at least one node in the edge
-is part of the cluster.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">[e]</div></div>
-<div class=" item_text " style="margin-left:3em">
-<p style="margin-top:0em; margin-bottom:0em">
-The projection value for start cluster x and end cluster y
-is the sum of edge weights of edges between x and y as a fraction
-of the sum of all edge weights of edges leaving x.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a name="pcfgcmce">[1]</a>
-Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a>
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/clmimac.1 b/doc/clmimac.1
deleted file mode 100644
index a32c0d3..0000000
--- a/doc/clmimac.1
+++ /dev/null
@@ -1,120 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm imac" 1 "16 May 2014" "clm imac 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
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-.br
-'in +\\$1
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-..
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-..
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-.am SH
-.ie n .in 4m
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-..
-.SH NAME
-clm imac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) As Clusterings\&.
-
-clmimac is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIimac\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm imac\fP -imx <fname> [options]
-
-\fBclm imac\fP
-\fB-imx\fP fname (\fIinput file\fP)
-\fB[-o\fP fname (\fIname/stem for output\fP)\fB]\fP
-\fB[-dag\fP fname (\fIoutput DAG\fP)\fB]\fP
-\fB[-overlap\fP str (\fIoverlap mode\fP)\fB]\fP
-\fB[-sort\fP str (\fIsize|revsize|lex|none\fP)\fB]\fP
-\fB[-strict\fP num (\fIin 0\&.\&.1\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-Use \fBclm imac\fP to interpret matrices (as clusterings) output by \fBmcl\fP using
-\fBmcl\fP\&'s \fB-dump\fP\ \&\fBite\fP option\&.
-
-Use \fBclm imac\fP only if you have a special reason; the normal usage
-of \fBmcl\fP is to do multiple runs for varying \fB-I\fP parameters
-and use the clusterings output by \fBmcl\fP itself\&.
-One reason is if you are interested in clusterings with overlap;
-early MCL iterands generally induce clusterings possessing overlap\&.
-Another reason is to investigate how the cluster structure
-associated with the MCL process evolves over time\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP fname (\fIinput file\fP)"
-\&
-.br
-The input file is presumably an MCL iterand resulting
-from the mcl option \fB-dump\fP\ \&\fBite\fP\&.
-.in -2m
-
-.ZI 2m "\fB-strict\fP num (\fIin 0\&.\&.1\fP)"
-\&
-.br
-Higher values (up until 1) will thin out the DAG
-constructed by \fBclm imac\fP\&. The default value is 0\&.00001,
-yielding the full DAG\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIfile name/stem\fP)"
-\&
-.br
-Write to file named \fIfname\fP\&.
-.in -2m
-
-.ZI 2m "\fB-dag\fP fname (\fIoutput DAG\fP)"
-\&
-.br
-Write the DAG (directed acyclic graph) constructed from the input to
-file\&. This DAG is constructed according to the structure associated
-with diagonally positive semi-definite matrices as described
-in the PhD thesis \fIGraph clustering by flow simulation\fP\&.
-Consult \fBmclfamily(7)\fP for references\&.
-.in -2m
-
-.ZI 2m "\fB-sort\fP str (\fIsize|revsize|lex|none\fP)"
-\&
-.br
-Sort the clusters either by increasing size, decreasing size,
-lexicographically by the indices they contain, or use the clustering
-exactly as obtained from the interpretation routine\&.
-.in -2m
-
-.ZI 2m "\fB-overlap\fP mode (\fIoverlap mode\fP)"
-\&
-.br
-With \fImode\fP set to \fIcut\fP, remove any overlap by allocating the
-nodes in overlap to the first cluster in which they were found\&. Mode
-\fIkeep\fP leaves overlap unchanged, and mode \fIsplit\fP results in overlapping
-parts excised and introduced as clusters in their own right\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmimac.html b/doc/clmimac.html
deleted file mode 100644
index 4f87cbf..0000000
--- a/doc/clmimac.html
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-<title>The clm imac manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmimac.ps"><b>clm imac</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm imac — Interpret Matrices (c.q. MCL iterands output by <b>mcl</b>) As Clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">clmimac is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>imac</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm imac</b> -imx <fname> [options]
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm imac</b>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input file</i>)</a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>name/stem for output</i>)<b>]</b></a>
-<a class="intern" href="#opt-dag"><b>[-dag</b> fname (<i>output DAG</i>)<b>]</b></a>
-<a class="intern" href="#opt-overlap"><b>[-overlap</b> str (<i>overlap mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-sort"><b>[-sort</b> str (<i>size|revsize|lex|none</i>)<b>]</b></a>
-<a class="intern" href="#opt-strict"><b>[-strict</b> num (<i>in 0..1</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-Use <b>clm imac</b> to interpret matrices (as clusterings) output by <b>mcl</b> using
-<b>mcl</b>'s <b>-dump</b> <b>ite</b> option.</p>
-<p style="margin-bottom:0" class="asd_par">
-Use <b>clm imac</b> only if you have a special reason; the normal usage
-of <b>mcl</b> is to do multiple runs for varying <b>-I</b> parameters
-and use the clusterings output by <b>mcl</b> itself.
-One reason is if you are interested in clusterings with overlap;
-early MCL iterands generally induce clusterings possessing overlap.
-Another reason is to investigate how the cluster structure
-associated with the MCL process evolves over time.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The input file is presumably an MCL iterand resulting
-from the mcl option <b>-dump</b> <b>ite</b>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-strict"></a><b>-strict</b> num (<i>in 0..1</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Higher values (up until 1) will thin out the DAG
-constructed by <b>clm imac</b>. The default value is 0.00001,
-yielding the full DAG.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>file name/stem</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write to file named <i>fname</i>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dag"></a><b>-dag</b> fname (<i>output DAG</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the DAG (directed acyclic graph) constructed from the input to
-file. This DAG is constructed according to the structure associated
-with diagonally positive semi-definite matrices as described
-in the PhD thesis <i>Graph clustering by flow simulation</i>.
-Consult <a class="local sibling" href="mclfamily.html">mclfamily</a> for references.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sort"></a><b>-sort</b> str (<i>size|revsize|lex|none</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sort the clusters either by increasing size, decreasing size,
-lexicographically by the indices they contain, or use the clustering
-exactly as obtained from the interpretation routine.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-overlap"></a><b>-overlap</b> mode (<i>overlap mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-With <i>mode</i> set to <i>cut</i>, remove any overlap by allocating the
-nodes in overlap to the first cluster in which they were found. Mode
-<i>keep</i> leaves overlap unchanged, and mode <i>split</i> results in overlapping
-parts excised and introduced as clusters in their own right.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/clminfo.1 b/doc/clminfo.1
deleted file mode 100644
index 953140f..0000000
--- a/doc/clminfo.1
+++ /dev/null
@@ -1,187 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm info" 1 "16 May 2014" "clm info 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm info \- compute performance measures for graphs and clusterings\&.
-
-clminfo is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIinfo\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm info\fP [options] <graph file> <cluster file> <cluster file>*
-
-\fBclm info\fP
-\fB[-o\fP fname (\fIwrite to file \fBfname\fP\fP)\fB]\fP
-\fB[-pi\fP f (\fIapply inflation beforehand\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-cl-tree\fP fname (\fIexpect file with nested clusterings\fP)\fB]\fP
-\fB[-cat-max\fP num (\fIdo at most \fBnum\fP tree levels\fP)\fB]\fP
-\fB[-cl-ceil\fP <num> (\fIskip clusters of size exceeding <num>\fP)\fB]\fP
-\fB[--node-self-measures\fP (\fIdump measure for native cluster\fP)\fB]\fP
-\fB[--node-all-measures\fP (\fIdump measure for incident cluster\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-<matrix file> <cluster file> <cluster file>*
-.SH DESCRIPTION
-
-\fBclm info\fP computes several numbers indicative for the efficiency with
-with a clustering captures the edge mass of a given graph\&.
-Use it in conjunction with \fBclm dist\fP to determine which clusterings
-you accept\&. See the EXAMPLES section in \fBclm dist\fP
-for an example of \fBclm dist\fP and \fBclm info\fP (and \fBclm meet\fP) usage\&.
-Output can be generated for multiple clusterings at the same time\&.
-
-The \fBefficiency\fP factor is described in [1] (see
-the \fBREFERENCES\fP section)\&. It tries to balance the dual aims of
-capturing a lot of edges or edge weights and keeping the cluster footprint
-or area fraction small\&. The efficiency number has several appealing
-mathematical properties, cf\&. [1]\&. It is related to, but not derivable from,
-the second and third numbers, the \fImass fraction\fP and the
-\fIarea fraction\fP\&.
-
-The \fBmass fraction\fP is defined as follows\&.
-Let \fBe\fP be an edge of the graph\&. The clustering \fIcaptures\fP \fBe\fP
-if the two nodes associated with \fBe\fP are in the same cluster\&.
-Now the mass fraction is the joint weight of all captured edges divided
-by the joint weight of all edges in the input graph\&.
-
-The \fBarea fraction\fP is roughly the sum of the
-squares of all cluster sizes for all clusters in the clustering, divided by
-the square of the number of nodes in the graph\&. It says \fIroughly\fP,
-because the actual formula uses the quantity \fBN\fP*(\fBN-1\fP) wherever it
-says square (of \fBN\fP) above\&. A low/high area fraction indicates a
-fine-grained/coarse clustering\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file name\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-pi\fP f (\fIapply inflation beforehand\fP)"
-\&
-.br
-Apply inflation to the graph matrix and compute the performance
-measures for the result\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-.br
-shared_defopt{-tf}
-.in -2m
-
-.ZI 2m "\fB-cl-tree\fP fname (\fIexpect file with nested clusterings (cone format)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cl-ceil\fP <num> (\fIskip (nested) clusters of size exceeding <num>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The specified file should contain a hierarchy of nested
-clusterings such as generated by \fBmclcm\fP\&. The output is then
-in a special format, undocumented but easy to understand\&.
-Its purpose is to help cherrypick a single clustering
-from a tree, in conjunction with the slightly experimental
-and undocumented program \fBmlmfifofum\fP\&.
-
-The measure that is used is very slow to compute for large clusters, and
-generally it will be outside any interesting range (i\&.e\&. it will be small)\&.
-Use \fB-cl-ceil\fP to skip clusters exceeding the specified size \-
-\fBclm info\fP will directly proceed to subclusters if they exist\&.
-.in -2m
-
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-\&
-.br
-This only has effect when used with \fB-cl-tree\fP\&.
-\fBclm info\fP will start at the most fine-grained level, working upwards\&.
-.in -2m
-
-.ZI 2m "\fB--node-all-measures\fP (\fIdump node-wise criteria for all incident clusters\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--node-self-measures\fP (\fIdump node-wise criteria for native cluster\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options return a key-value based format, with the meaning of
-the keys as follows\&.
-
-.di ZV
-.in 0
-.nf \fC
-nm file name (redundant unless multiple cluster files are provided)
-ni node index
-ci cluster index
-nn number of neighbours of this node (constant for a give node)
-nc cluster size (constant for a given cluster)
-ef efficiency for this node/cluster combination
-em max-efficiency for this node/cluster combination
-mf mass fraction: percentage of edge weights for this node in this cluster
-ma total mass of edge weights for this node in this cluster
-xn number of neighbours of the node that are not in the cluster
-xc number of nodes in the cluster that are not a neighbour of the node
-ns number of neighbours of the node that are also in this cluster
-ti the maximum of the edge weights for neighbours of this node that are in this cluster
-to the maximum of the edge weights for neighbours of this node that are NOT in this cluster
-al (alien) 1 if the node is not native to the cluster, 0 if the node is native
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
-.SH REFERENCES
-
-[1] Stijn van Dongen\&. \fIPerformance criteria for graph clustering and Markov
-cluster experiments\fP\&. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0012\&.ps\&.Z
diff --git a/doc/clminfo.html b/doc/clminfo.html
deleted file mode 100644
index 35a9e94..0000000
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-<title>The clm info manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clminfo.ps"><b>clm info</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#_section_4">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm info — compute performance measures for graphs and clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">clminfo is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>info</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info</b> [options] <graph file> <cluster file> <cluster file>*
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info</b>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>write to file <b>fname</b></i>)<b>]</b></a>
-<a class="intern" href="#opt-pi"><b>[-pi</b> f (<i>apply inflation beforehand</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-cl-tree"><b>[-cl-tree</b> fname (<i>expect file with nested clusterings</i>)<b>]</b></a>
-<a class="intern" href="#opt-cat-max"><b>[-cat-max</b> num (<i>do at most <b>num</b> tree levels</i>)<b>]</b></a>
-<a class="intern" href="#opt-cl-ceil"><b>[-cl-ceil</b> <num> (<i>skip clusters of size exceeding <num></i>)<b>]</b></a>
-<a class="intern" href="#opt--node-self-measures"><b>[--node-self-measures</b> (<i>dump measure for native cluster</i>)<b>]</b></a>
-<a class="intern" href="#opt--node-all-measures"><b>[--node-all-measures</b> (<i>dump measure for incident cluster</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<matrix file> <cluster file> <cluster file>*
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info</b> computes several numbers indicative for the efficiency with
-with a clustering captures the edge mass of a given graph.
-Use it in conjunction with <b>clm dist</b> to determine which clusterings
-you accept. See the EXAMPLES section in <b>clm dist</b>
-for an example of <b>clm dist</b> and <b>clm info</b> (and <b>clm meet</b>) usage.
-Output can be generated for multiple clusterings at the same time.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>efficiency</b> factor is described in [1] (see
-the <a class="intern" href="#references">REFERENCES</a> section). It tries to balance the dual aims of
-capturing a lot of edges or edge weights and keeping the cluster footprint
-or area fraction small. The efficiency number has several appealing
-mathematical properties, cf. [1]. It is related to, but not derivable from,
-the second and third numbers, the <i>mass fraction</i> and the
-<i>area fraction</i>.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>mass fraction</b> is defined as follows.
-Let <b>e</b> be an edge of the graph. The clustering <i>captures</i> <b>e</b>
-if the two nodes associated with <b>e</b> are in the same cluster.
-Now the mass fraction is the joint weight of all captured edges divided
-by the joint weight of all edges in the input graph.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>area fraction</b> is roughly the sum of the
-squares of all cluster sizes for all clusters in the clustering, divided by
-the square of the number of nodes in the graph. It says <i>roughly</i>,
-because the actual formula uses the quantity <b>N</b>*(<b>N-1</b>) wherever it
-says square (of <b>N</b>) above. A low/high area fraction indicates a
-fine-grained/coarse clustering.</p>
-
-<a name="_section_4"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-pi"></a><b>-pi</b> f (<i>apply inflation beforehand</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Apply inflation to the graph matrix and compute the performance
-measures for the result.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">shared_defopt{-tf}</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cl-tree"></a><b>-cl-tree</b> fname (<i>expect file with nested clusterings (cone format)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cl-ceil"></a><b>-cl-ceil</b> <num> (<i>skip (nested) clusters of size exceeding <num></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The specified file should contain a hierarchy of nested
-clusterings such as generated by <b>mclcm</b>. The output is then
-in a special format, undocumented but easy to understand.
-Its purpose is to help cherrypick a single clustering
-from a tree, in conjunction with the slightly experimental
-and undocumented program <b>mlmfifofum</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The measure that is used is very slow to compute for large clusters, and
-generally it will be outside any interesting range (i.e. it will be small).
-Use <b>-cl-ceil</b> to skip clusters exceeding the specified size —
-<b>clm info</b> will directly proceed to subclusters if they exist.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cat-max"></a><b>-cat-max</b> num (<i>do at most num levels</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This only has effect when used with <b>-cl-tree</b>.
-<b>clm info</b> will start at the most fine-grained level, working upwards.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--node-all-measures"></a><b>--node-all-measures</b> (<i>dump node-wise criteria for all incident clusters</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--node-self-measures"></a><b>--node-self-measures</b> (<i>dump node-wise criteria for native cluster</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options return a key-value based format, with the meaning of
-the keys as follows.
-</p>
-<div class="verbatim">nm file name (redundant unless multiple cluster files are provided)
-ni node index
-ci cluster index
-nn number of neighbours of this node (constant for a give node)
-nc cluster size (constant for a given cluster)
-ef efficiency for this node/cluster combination
-em max-efficiency for this node/cluster combination
-mf mass fraction: percentage of edge weights for this node in this cluster
-ma total mass of edge weights for this node in this cluster
-xn number of neighbours of the node that are not in the cluster
-xc number of nodes in the cluster that are not a neighbour of the node
-ns number of neighbours of the node that are also in this cluster
-ti the maximum of the edge weights for neighbours of this node that are in this cluster
-to the maximum of the edge weights for neighbours of this node that are NOT in this cluster
-al (alien) 1 if the node is not native to the cluster, 0 if the node is native</div>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-[1] Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
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diff --git a/doc/clminfo2.1 b/doc/clminfo2.1
deleted file mode 100644
index be94a18..0000000
--- a/doc/clminfo2.1
+++ /dev/null
@@ -1,199 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm info2" 1 "16 May 2014" "clm info2 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm info2 \- compute performance measures for graphs and clusterings\&.
-
-clminfo2 is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIinfo2\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm info2\fP [options] <graph file> <cluster file> <cluster file>*
-
-\fBclm info2\fP
-\fB[-o\fP fname (\fIwrite to file \fBfname\fP\fP)\fB]\fP
-\fB[-pi\fP f (\fIapply inflation beforehand\fP)\fB]\fP
-\fB[--list\fP (\fIlist efficiency for all nodes\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-cl-ceil\fP <num> (\fIskip clusters of size exceeding \fB<num>\fP\fP)\fB]\fP
-\fB[-cat-max\fP <num> (\fIdo at most \fB<num>\fP tree levels\fP)\fB]\fP
-\fB[-cl-tree\fP fname (\fIexpect file with nested clusterings\fP)\fB]\fP
-\fB[-t\fP <int> (\fIuse <int> threads\fP)\fB]\fP
-\fB[-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)\fB]\fP
-\fB[-j\fP <intj> (\fIthis job has index <intj>\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-<matrix file> <cluster file> <cluster file>*
-.SH DESCRIPTION
-
-\fBclm info2\fP is a streamlined and updated version of \fBclm info\fP\&. The
-latter outputs a key-value format listing a number of measures\&. In contrast,
-\fBclm info2\fP only outputs the so-called efficiency criterion, a quality
-index for networks and clusterings\&. This criterion can be generated for
-each node independently with the \fB--list\fP option, indicating how
-well a clustering captures the neighbour distribution of a given node\&.
-
-\fBclm info2\fP can utilise threading and job dispatching\&. This may be useful
-when dealing with very large graphs\&.
-
-Multiple clusterings can be supplied on the command-line\&.
-Output is tabular, each row corresponding with a clustering in the
-ordering as supplied on the command line\&. Multiple columns will
-result only if node-wise output is induced with \fB--list\fP\&.
-By default a single number is produced for each individual clustering:
-the mean of all node-wise scores for that clustering\&.
-
-The \fBefficiency\fP factor is described in [1] (see
-the \fBREFERENCES\fP section)\&. It tries to balance the dual aims of
-capturing a lot of edges or edge weights and keeping the cluster footprint
-or area fraction small\&. The efficiency number has several appealing
-mathematical properties, cf\&. [1]\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file name\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-pi\fP f (\fIapply inflation beforehand\fP)"
-\&
-.br
-Apply inflation to the graph matrix and compute the performance
-measures for the result\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-.br
-shared_defopt{-tf}
-.in -2m
-
-.ZI 2m "\fB--list\fP (\fIlist efficiency for all nodes\fP)"
-\&
-.br
-The efficiency scores for all nodes are given on a single line\&.
-Each clustering specified corresponds to a single line\&.
-.in -2m
-
-.ZI 2m "\fB-cl-tree\fP fname (\fIexpect file with nested clusterings (cone format)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cl-ceil\fP <num> (\fIskip (nested) clusters of size exceeding <num>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The specified file should contain a hierarchy of nested
-clusterings such as generated by \fBmclcm\fP\&. The output is then
-in a special format, undocumented but easy to understand\&.
-Its purpose is to help cherrypick a single clustering
-from a tree, in conjunction with the slightly experimental
-and undocumented program \fBmlmfifofum\fP\&.
-
-The measure that is used is very slow to compute for large clusters, and
-generally it will be outside any interesting range (i\&.e\&. it will be small)\&.
-Use \fB-cl-ceil\fP to skip clusters exceeding the specified size \-
-\fBclm info\fP will directly proceed to subclusters if they exist\&.
-.in -2m
-
-.ZI 2m "\fB-cat-max\fP num (\fIdo at most num levels\fP)"
-\&
-.br
-This only has effect when used with \fB-cl-tree\fP\&.
-\fBclm info\fP will start at the most fine-grained level, working upwards\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <int> (\fIuse <int> threads\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-j\fP <intj> (\fIthis job has index <intj>\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-For very large graphs (millions of nodes) and clusterings with large
-clusters it may be helpful to allow this program to use multiple CPUs\&.
-Additionally it is possible to spread the computation over multiple
-jobs/machines\&. These three options are described in the \fBclmprotocols\fP manual page\&.
-The following set of options, if given to as many commands, defines three jobs, each running four threads\&.
-
-.di ZV
-.in 0
-.nf \fC
--t 4 -J 3 -j 0 -o out\&.0
--t 4 -J 3 -j 1 -o out\&.1
--t 4 -J 3 -j 2 -o out\&.2
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The output can then be collected with
-
-.di ZV
-.in 0
-.nf \fC
-clxdo add_table out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
-.SH REFERENCES
-
-[1] Stijn van Dongen\&. \fIPerformance criteria for graph clustering and Markov
-cluster experiments\fP\&. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0012\&.ps\&.Z
diff --git a/doc/clminfo2.html b/doc/clminfo2.html
deleted file mode 100644
index 2731742..0000000
--- a/doc/clminfo2.html
+++ /dev/null
@@ -1,264 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
-margin-right: 0%;
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-a:link { text-decoration: none; }
-a:active { text-decoration: none; }
-a:visited { text-decoration: none; }
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-a.local:link { color: #11aa11; }
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-a.extern:link { color: #aa1111; }
-a.extern:active { color: #aa1111; }
-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
-}
-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
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-.item_rightalign
-{ width: 2em;
-text-align: right;
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-.item_compact .item_rightalign
-{ position: absolute;
-width: 52em;
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-margin-left: 3em;
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-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
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-}
-</style>
-<title>The clm info2 manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clminfo2.ps"><b>clm info2</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#_section_4">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm info2 — compute performance measures for graphs and clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">clminfo2 is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>info2</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info2</b> [options] <graph file> <cluster file> <cluster file>*
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info2</b>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>write to file <b>fname</b></i>)<b>]</b></a>
-<a class="intern" href="#opt-pi"><b>[-pi</b> f (<i>apply inflation beforehand</i>)<b>]</b></a>
-<a class="intern" href="#opt--list"><b>[--list</b> (<i>list efficiency for all nodes</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-cl-ceil"><b>[-cl-ceil</b> <num> (<i>skip clusters of size exceeding <b><num></b></i>)<b>]</b></a>
-<a class="intern" href="#opt-cat-max"><b>[-cat-max</b> <num> (<i>do at most <b><num></b> tree levels</i>)<b>]</b></a>
-<a class="intern" href="#opt-cl-tree"><b>[-cl-tree</b> fname (<i>expect file with nested clusterings</i>)<b>]</b></a>
-<a class="intern" href="#opt-t"><b>[-t</b> <int> (<i>use <int> threads</i>)<b>]</b></a>
-<a class="intern" href="#opt-J"><b>[-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)<b>]</b></a>
-<a class="intern" href="#opt-j"><b>[-j</b> <intj> (<i>this job has index <intj></i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<matrix file> <cluster file> <cluster file>*
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info2</b> is a streamlined and updated version of <b>clm info</b>. The
-latter outputs a key-value format listing a number of measures. In contrast,
-<b>clm info2</b> only outputs the so-called efficiency criterion, a quality
-index for networks and clusterings. This criterion can be generated for
-each node independently with the <b>--list</b> option, indicating how
-well a clustering captures the neighbour distribution of a given node.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm info2</b> can utilise threading and job dispatching. This may be useful
-when dealing with very large graphs.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Multiple clusterings can be supplied on the command-line.
-Output is tabular, each row corresponding with a clustering in the
-ordering as supplied on the command line. Multiple columns will
-result only if node-wise output is induced with <b>--list</b>.
-By default a single number is produced for each individual clustering:
-the mean of all node-wise scores for that clustering.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>efficiency</b> factor is described in [1] (see
-the <a class="intern" href="#references">REFERENCES</a> section). It tries to balance the dual aims of
-capturing a lot of edges or edge weights and keeping the cluster footprint
-or area fraction small. The efficiency number has several appealing
-mathematical properties, cf. [1].</p>
-
-<a name="_section_4"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-pi"></a><b>-pi</b> f (<i>apply inflation beforehand</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Apply inflation to the graph matrix and compute the performance
-measures for the result.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">shared_defopt{-tf}</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--list"></a><b>--list</b> (<i>list efficiency for all nodes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The efficiency scores for all nodes are given on a single line.
-Each clustering specified corresponds to a single line.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cl-tree"></a><b>-cl-tree</b> fname (<i>expect file with nested clusterings (cone format)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cl-ceil"></a><b>-cl-ceil</b> <num> (<i>skip (nested) clusters of size exceeding <num></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The specified file should contain a hierarchy of nested
-clusterings such as generated by <b>mclcm</b>. The output is then
-in a special format, undocumented but easy to understand.
-Its purpose is to help cherrypick a single clustering
-from a tree, in conjunction with the slightly experimental
-and undocumented program <b>mlmfifofum</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The measure that is used is very slow to compute for large clusters, and
-generally it will be outside any interesting range (i.e. it will be small).
-Use <b>-cl-ceil</b> to skip clusters exceeding the specified size —
-<b>clm info</b> will directly proceed to subclusters if they exist.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cat-max"></a><b>-cat-max</b> num (<i>do at most num levels</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This only has effect when used with <b>-cl-tree</b>.
-<b>clm info</b> will start at the most fine-grained level, working upwards.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-t"></a><b>-t</b> <int> (<i>use <int> threads</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-j"></a><b>-j</b> <intj> (<i>this job has index <intj></i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-J"></a><b>-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-For very large graphs (millions of nodes) and clusterings with large
-clusters it may be helpful to allow this program to use multiple CPUs.
-Additionally it is possible to spread the computation over multiple
-jobs/machines. These three options are described in the <a class="local sibling" href="clmprotocols.html">clmprotocols</a> manual page.
-The following set of options, if given to as many commands, defines three jobs, each running four threads.
-</p>
-<div class="verbatim">-t 4 -J 3 -j 0 -o out.0
--t 4 -J 3 -j 1 -o out.1
--t 4 -J 3 -j 2 -o out.2</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output can then be collected with
-</p>
-<div class="verbatim">clxdo add_table out.[0-2]</div>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-[1] Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
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diff --git a/doc/clmmate.1 b/doc/clmmate.1
deleted file mode 100644
index c09bd6f..0000000
--- a/doc/clmmate.1
+++ /dev/null
@@ -1,146 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm mate" 1 "16 May 2014" "clm mate 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm mate \- compute best matches between two clusterings
-
-clmmate is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fImate\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm mate\fP
-\fB[-o\fP fname (\fIoutput file name\fP)\fB]\fP
-\fB[-b\fP (\fIomit headers\fP)\fB]\fP
-\fB[--one-to-many\fP (\fIrequire multiple hits in <clfile1>\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-<clfile1> <clfile2>
-.SH DESCRIPTION
-
-\fBclm mate\fP computes for each cluster \fCX\fP in \fCclfile1\fP all clusters
-\fCY\fP in \fCclfile2\fP that have non-empty intersection and outputs
-a line with the data points listed below\&.
-
-.di ZV
-.in 0
-.nf \fC
- overlap(X,Y) # 2 * size(meet(X,Y)) / (size(X)+size(Y))
- index(X) # name of cluster
- index(Y) # name of cluster
- size(meet(X,Y))
- size(X-Y) # size of left difference
- size(Y-X) # size of right difference
- size(X)
- size(Y)
- projection(X, clfile2) # see below
- projection(Y, clfile1) # see below
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The projected size of a cluster \fCX\fP relative to a clustering \fCK\fP is
-simply the sum of all the nodes shared between any cluster \fCY\fP in \fCK\fP
-and \fCX\fP, duplications allowed\&. For example, the projected size of
-\fC(0,1)\fP relative to \fC{(0,2,4), (1,4,9), (1,3,5)}\fP equals \fC3\fP\&.
-
-The overlap between \fCX\fP and \fCY\fP is exactly
-1\&.0 if the two clusters are identical, and for nearly identical
-clusterings the score will be close to 1\&.0\&.
-
-All of this information can also be obtained from the
-contingency matrix defined for two clusterings\&.
-The \fC[i,j]\fP row-column entry in a contigency matrix between
-to clusterings gives the number of entries in the intersection
-between cluster\ \&\fCi\fP and cluster\ \&\fCj\fP from the respective
-clusterings\&. The other information is implicitly present;
-the total number of nodes in clusters\ \&\fCi\fP and\ \&\fCj\fP
-for example can be obtained as the sum of entries in row\ \&\fCi\fP
-and column\ \&\fCj\fP respectively, and the difference counts
-can then be obtained by substracting the intersection count\&.
-The contingency matrix can easily be computed using \fBmcx\fP;
-e\&.g\&.
-
-.di ZV
-.in 0
-.nf \fC
-
-mcx /clfile2 lm /clfile1 lm tp mul /ting wm
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-will create the contingency matrix in mcl matrix format
-in the file \fCting\fP, where columns range over the clusters
-in \fCclfile1\fP\&.
-
-The output can be put to good use by sorting it numerically on
-that first score field\&. It is advisable to use a stable sort routine
-(use the \fB-s\fP option for UNIX sort)
-From this information one can quickly extract the closest
-clusters between two clusterings\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file name\fP)"
-\&
-.br
-Specify the name of the output file\&.
-.in -2m
-
-.ZI 2m "\fB-b\fP (\fIomit headers\fP)"
-\&
-.br
-Batch mode, omit column names\&.
-.in -2m
-
-.ZI 2m "\fB--one-to-many\fP (\fIrequire multiple hits in <clfile1>\fP)"
-\&
-.br
-Do not output information for clusters in the first file
-that are subset of a cluster in the second file\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmmate.html b/doc/clmmate.html
deleted file mode 100644
index 68c4c56..0000000
--- a/doc/clmmate.html
+++ /dev/null
@@ -1,218 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
-margin-right: 0%;
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-a.local:link { color: #11aa11; }
-a.local:active { color: #11aa11; }
-a.local:visited { color: #116611; }
-a.intern:link { color: #1111aa; }
-a.intern:active { color: #1111aa; }
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-a.extern:link { color: #aa1111; }
-a.extern:active { color: #aa1111; }
-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
-}
-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
-.item_leftalign { text-align: left; }
-.item_rightalign
-{ width: 2em;
-text-align: right;
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-.item_compact .item_rightalign
-{ position: absolute;
-width: 52em;
-right: -2em;
-text-align: right;
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-{ position: relative;
-margin-left: 3em;
-}
-.smallcaps { font-size: smaller; text-transform: uppercase }
-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
-margin-right: 8%;
-}
-</style>
-<title>The clm mate manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmmate.ps"><b>clm mate</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm mate — compute best matches between two clusterings</p>
-<p style="margin-bottom:0" class="asd_par">clmmate is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>mate</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm mate</b>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-b"><b>[-b</b> (<i>omit headers</i>)<b>]</b></a>
-<a class="intern" href="#opt--one-to-many"><b>[--one-to-many</b> (<i>require multiple hits in <clfile1></i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<clfile1> <clfile2>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm mate</b> computes for each cluster <tt>X</tt> in <tt>clfile1</tt> all clusters
-<tt>Y</tt> in <tt>clfile2</tt> that have non-empty intersection and outputs
-a line with the data points listed below.</p>
-<div class="verbatim"> overlap(X,Y) # 2 * size(meet(X,Y)) / (size(X)+size(Y))
- index(X) # name of cluster
- index(Y) # name of cluster
- size(meet(X,Y))
- size(X-Y) # size of left difference
- size(Y-X) # size of right difference
- size(X)
- size(Y)
- projection(X, clfile2) # see below
- projection(Y, clfile1) # see below
-</div>
-<p style="margin-bottom:0" class="asd_par">
-The projected size of a cluster <tt>X</tt> relative to a clustering <tt>K</tt> is
-simply the sum of all the nodes shared between any cluster <tt>Y</tt> in <tt>K</tt>
-and <tt>X</tt>, duplications allowed. For example, the projected size of
-<tt>(0,1)</tt> relative to <tt>{(0,2,4), (1,4,9), (1,3,5)}</tt> equals <tt>3</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-The overlap between <tt>X</tt> and <tt>Y</tt> is exactly
-1.0 if the two clusters are identical, and for nearly identical
-clusterings the score will be close to 1.0.</p>
-<p style="margin-bottom:0" class="asd_par">
-All of this information can also be obtained from the
-contingency matrix defined for two clusterings.
-The <tt>[i,j]</tt> row-column entry in a contigency matrix between
-to clusterings gives the number of entries in the intersection
-between cluster <tt>i</tt> and cluster <tt>j</tt> from the respective
-clusterings. The other information is implicitly present;
-the total number of nodes in clusters <tt>i</tt> and <tt>j</tt>
-for example can be obtained as the sum of entries in row <tt>i</tt>
-and column <tt>j</tt> respectively, and the difference counts
-can then be obtained by substracting the intersection count.
-The contingency matrix can easily be computed using <b>mcx</b>;
-e.g.</p>
-<div class="verbatim">
-mcx /clfile2 lm /clfile1 lm tp mul /ting wm</div>
-<p style="margin-top:0em; margin-bottom:0em">
-will create the contingency matrix in mcl matrix format
-in the file <tt>ting</tt>, where columns range over the clusters
-in <tt>clfile1</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-The output can be put to good use by sorting it numerically on
-that first score field. It is advisable to use a stable sort routine
-(use the <b>-s</b> option for UNIX sort)
-From this information one can quickly extract the closest
-clusters between two clusterings.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">Specify the name of the output file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-b"></a><b>-b</b> (<i>omit headers</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">Batch mode, omit column names.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--one-to-many"></a><b>--one-to-many</b> (<i>require multiple hits in <clfile1></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">Do not output information for clusters in the first file
-that are subset of a cluster in the second file.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
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diff --git a/doc/clmmeet.1 b/doc/clmmeet.1
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-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm meet" 1 "16 May 2014" "clm meet 14-137" "USER COMMANDS "
-.po 2m
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-..
-.SH NAME
-clm meet \- compute the intersection of a set of clusterings\&.
-
-clmmeet is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fImeet\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm meet\fP
-\fB[-o\fP fname (\fIoutput file name\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-<file name>+
-.SH DESCRIPTION
-
-\fBclm meet\fP computes the intersection of a set of clusterings, that is,
-the largest clustering that is a subclustering of all the clusterings
-in the set\&. It stores the intersection (or meet) in the argument
-to the \fB-o\fP flag, which must be the first option given\&.
-All remaining arguments are interpreted as names of files containing
-clusterings in mcl format (see \fBmcxio(5)\fP), which must all
-pertain to a set of the same cardinality\&.
-
-This utility can be useful in measuring (in conjunction with
-\fBclm\ \&dist\fP) the consistency of a set of clusterings at different
-levels of granularity \- if the meet of all those clusterings is close to
-being a subclustering of each of them, consistency is good\&. See
-\fBclm\ \&dist\fP for an example\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file name\fP)"
-\&
-.br
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmmeet.html b/doc/clmmeet.html
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-<title>The clm meet manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmmeet.ps"><b>clm meet</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm meet — compute the intersection of a set of clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">clmmeet is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>meet</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm meet</b>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<file name>+
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm meet</b> computes the intersection of a set of clusterings, that is,
-the largest clustering that is a subclustering of all the clusterings
-in the set. It stores the intersection (or meet) in the argument
-to the <b>-o</b> flag, which must be the first option given.
-All remaining arguments are interpreted as names of files containing
-clusterings in mcl format (see <a class="local sibling" href="mcxio.html">mcxio</a>), which must all
-pertain to a set of the same cardinality.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This utility can be useful in measuring (in conjunction with
-<a class="local sibling" href="clmdist.html">clm dist</a>) the consistency of a set of clusterings at different
-levels of granularity — if the meet of all those clusterings is close to
-being a subclustering of each of them, consistency is good. See
-<a class="local sibling" href="clmdist.html">clm dist</a> for an example.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/clmoptics.1 b/doc/clmoptics.1
deleted file mode 100644
index 23d0708..0000000
--- a/doc/clmoptics.1
+++ /dev/null
@@ -1,145 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm optics" 1 "16 May 2014" "clm optics 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
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-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
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-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm optics \- implementation of the OPTICS reachability ordering
-
-clmoptics is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIoptics\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm optics\fP -imx <fname> [options]
-
-\fBclm optics\fP
-\fB-imx\fP fname (\fIinput graph file name\fP)
-\fB-max-eps\fP <num> (\fImaximum distance considered\fP)
-\fB-min-eps\fP <num> (\fIminimum similarity considered\fP)
-\fB-min-pts\fP <int> (\fIminimum eps-neighbourhood size\fP)
-\fB[-icl\fP fname (\fIinput clustering name\fP)\fB]\fP
-\fB[-o\fP fname (\fIoutput name\fP)\fB]\fP
-\fB[-ps\fP fname (\fIPostScript output name\fP)\fB]\fP
-\fB[-psx\fP fname (\fIscaling factor x axis\fP)\fB]\fP
-\fB[-psy\fP fname (\fIscaling factor y axis\fP)\fB]\fP
-\fB[-ps-rows\fP <num> (\fIsplit reachability plot into <num> rows\fP)\fB]\fP
-\fB[--ps-labels\fP (\fIshow identifiers in PS output\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-This programs computes the reachability ordering according to the \fBOPTICS\fP
-clustering method\&. It can additionally output a PostScript plot of the reachability
-landscape\&. This plot can be annotated with a user-supplied clustering\&.
-The program does not implement the clustering method that is associated
-with \fBOPTICS\fP\&. It is part of \fBmcl-edge\fP primarily as a visualisation aid\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP fname (\fIinput file\fP)"
-\&
-.br
-The input file, encoding a graph in native format\&.
-.in -2m
-
-.ZI 2m "\fB-max-eps\fP <num> (\fImaximum distance considered\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-min-eps\fP <num> (\fIminimum similarity considered\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-min-pts\fP <int> (\fIminimum eps-neighbourhood size\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These encode the \fBOPTICS\fP parameters\&. Use \fB-max-eps\fP if the
-edge weights encode a distance (for example the Euclidean distance between
-points), use \fB-min-eps\fP if the edge weights encode a similarity\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ps\fP fname (\fIPostScript file name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-icl\fP fname (\fIinput clustering name\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The \fB-o\fP\ \&\fIfname\fP option controls the name of the file in which the reachability
-values are written\&. By default these values are written to STDOUT\&.
-
-If \fB-ps\fP\ \&\fIfname\fP is supplied the program will additionally output a visualisation
-of the reachability landscape plot in a PostScript file\&.
-
-It is possible, in addition to \fB-ps\fP, to specify a clustering with \fB-icl\fP\ \&\fIfname\fP\&.
-Each vertical bar in the landscape plot will be coloured according to cluster membership,
-that is, nodes in the same cluster will have the same colour\&. This can be a useful way
-to visualise separation properties of clusterings\&.
-.in -2m
-
-.ZI 2m "\fB-psx\fP fname (\fIscaling factor x axis\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-psy\fP fname (\fIscaling factor y axis\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--ps-labels\fP (\fIshow identifiers in PS output\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ps-rows\fP <num> (\fIsplit reachability plot into <num> rows\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-By default the PostScript output will be scaled to fit onto an A3 page\&.
-The scaling options \fB-psx\fP and \fB-psy\fP can be used as additional
-scaling factors\&. By default these are set \fC1\&.0\fP\&.
-
-The \fB--ps-labels\fP can be used to annotate each vertical bar in the landscape
-plot with the \fBmcl-edge\fP identifier of the corresponding node\&.
-
-The \fB-ps-rows\fP option sets the number of rows\&. This is the primary
-option affect the width of a bar\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmoptics.html b/doc/clmoptics.html
deleted file mode 100644
index 327bae0..0000000
--- a/doc/clmoptics.html
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!-- Copyright (c) 2014 Stijn van Dongen -->
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-body
-{ text-align: justify;
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-</style>
-<title>The clm optics manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmoptics.ps"><b>clm optics</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm optics — implementation of the OPTICS reachability ordering</p>
-<p style="margin-bottom:0" class="asd_par">clmoptics is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>optics</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm optics</b> -imx <fname> [options]
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm optics</b>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input graph file name</i>)</a>
-<a class="intern" href="#opt-max-eps"><b>-max-eps</b> <num> (<i>maximum distance considered</i>)</a>
-<a class="intern" href="#opt-min-eps"><b>-min-eps</b> <num> (<i>minimum similarity considered</i>)</a>
-<a class="intern" href="#opt-min-pts"><b>-min-pts</b> <int> (<i>minimum eps-neighbourhood size</i>)</a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> fname (<i>input clustering name</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output name</i>)<b>]</b></a>
-<a class="intern" href="#opt-ps"><b>[-ps</b> fname (<i>PostScript output name</i>)<b>]</b></a>
-<a class="intern" href="#opt-psx"><b>[-psx</b> fname (<i>scaling factor x axis</i>)<b>]</b></a>
-<a class="intern" href="#opt-psy"><b>[-psy</b> fname (<i>scaling factor y axis</i>)<b>]</b></a>
-<a class="intern" href="#opt-ps-rows"><b>[-ps-rows</b> <num> (<i>split reachability plot into <num> rows</i>)<b>]</b></a>
-<a class="intern" href="#opt--ps-labels"><b>[--ps-labels</b> (<i>show identifiers in PS output</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-This programs computes the reachability ordering according to the <b>OPTICS</b>
-clustering method. It can additionally output a PostScript plot of the reachability
-landscape. This plot can be annotated with a user-supplied clustering.
-The program does not implement the clustering method that is associated
-with <b>OPTICS</b>. It is part of <b>mcl-edge</b> primarily as a visualisation aid.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The input file, encoding a graph in native format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-max-eps"></a><b>-max-eps</b> <num> (<i>maximum distance considered</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-min-eps"></a><b>-min-eps</b> <num> (<i>minimum similarity considered</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-min-pts"></a><b>-min-pts</b> <int> (<i>minimum eps-neighbourhood size</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These encode the <b>OPTICS</b> parameters. Use <b>-max-eps</b> if the
-edge weights encode a distance (for example the Euclidean distance between
-points), use <b>-min-eps</b> if the edge weights encode a similarity.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ps"></a><b>-ps</b> fname (<i>PostScript file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-icl"></a><b>-icl</b> fname (<i>input clustering name</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The <b>-o</b> <i>fname</i> option controls the name of the file in which the reachability
-values are written. By default these values are written to STDOUT.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If <b>-ps</b> <i>fname</i> is supplied the program will additionally output a visualisation
-of the reachability landscape plot in a PostScript file.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible, in addition to <b>-ps</b>, to specify a clustering with <b>-icl</b> <i>fname</i>.
-Each vertical bar in the landscape plot will be coloured according to cluster membership,
-that is, nodes in the same cluster will have the same colour. This can be a useful way
-to visualise separation properties of clusterings.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-psx"></a><b>-psx</b> fname (<i>scaling factor x axis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-psy"></a><b>-psy</b> fname (<i>scaling factor y axis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--ps-labels"></a><b>--ps-labels</b> (<i>show identifiers in PS output</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name= [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-By default the PostScript output will be scaled to fit onto an A3 page.
-The scaling options <b>-psx</b> and <b>-psy</b> can be used as additional
-scaling factors. By default these are set <tt>1.0</tt>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--ps-labels</b> can be used to annotate each vertical bar in the landscape
-plot with the <b>mcl-edge</b> identifier of the corresponding node.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-ps-rows</b> option sets the number of rows. This is the primary
-option affect the width of a bar.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/clmorder.1 b/doc/clmorder.1
deleted file mode 100644
index e6f8e29..0000000
--- a/doc/clmorder.1
+++ /dev/null
@@ -1,87 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm order" 1 "16 May 2014" "clm order 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm order \- reorder clusterings conformal to inclusion structure
-
-clmorder is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIorder\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm order\fP
-\fB[-prefix\fP <string> (\fIfile multiplex prefix\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIconcatenated output in single file\fP)\fB]\fP
-<cluster|stack>+
-.SH DESCRIPTION
-
-Given a set of input clusterings \fBclm order\fP first transform it into a stack
-of strictly nesting clusterings\&. It does this by splitting clusters where
-necessary\&.
-It then reorders the coarsest (i\&.e\&. level-one) clustering, from large to
-small clusters\&. After that it reorders the second coarsest clustering
-conformally such that the first batch among its reordered clusters covers the
-level-one largest cluster, the second batch covers the level-one second
-largest cluster, and so on\&. Within these constraints, each batch of
-second-level clusters (corresponding to a single first-level cluster) is
-again ordered from larger to smaller clusters\&. This process is applied
-recursively throughout the entire stack of input clusters\&.
-
-The input can be specified in multiple files, and a single file may contain
-multiple clusterings\&. The output is by default written as a concatenation of
-matrix files, the so-called stack format\&. Use the \fB-o\fP option to
-specify the output file\&. The stacked format can be converted to Newick
-format using \fBmcxdump(1)\fP\&. The output can be written to multiple files,
-one for each projected clustering, by using the \fB-prefix\fP option\&. By
-example, \fB-prefix\fP\ \&\fBP\fP leads to output in files named \fCP1\fP, \fCP2\fP,
-\&.\&.\fCPN\fP, where \fCN\fP is the number of clusters in the input, \fCP1\fP is the
-most fine-grained ordered clustering, and \fCPN\fP is the coarsest clustering\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-prefix\fP (\fI<string>\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-o\fP (\fI<fname>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-As decribed above\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmorder.html b/doc/clmorder.html
deleted file mode 100644
index d20b9f1..0000000
--- a/doc/clmorder.html
+++ /dev/null
@@ -1,182 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<!-- Copyright (c) 2014 Stijn van Dongen -->
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-a.extern:visited { color: #661111; }
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-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
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-font-size: 10pt;
-margin-left: 2em;
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-<title>The clm order manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmorder.ps"><b>clm order</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm order — reorder clusterings conformal to inclusion structure</p>
-<p style="margin-bottom:0" class="asd_par">clmorder is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>order</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm order</b>
-<a class="intern" href="#opt-prefix"><b>[-prefix</b> <string> (<i>file multiplex prefix</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>concatenated output in single file</i>)<b>]</b></a>
-<cluster|stack>+
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-Given a set of input clusterings <b>clm order</b> first transform it into a stack
-of strictly nesting clusterings. It does this by splitting clusters where
-necessary.
-It then reorders the coarsest (i.e. level-one) clustering, from large to
-small clusters. After that it reorders the second coarsest clustering
-conformally such that the first batch among its reordered clusters covers the
-level-one largest cluster, the second batch covers the level-one second
-largest cluster, and so on. Within these constraints, each batch of
-second-level clusters (corresponding to a single first-level cluster) is
-again ordered from larger to smaller clusters. This process is applied
-recursively throughout the entire stack of input clusters.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The input can be specified in multiple files, and a single file may contain
-multiple clusterings. The output is by default written as a concatenation of
-matrix files, the so-called stack format. Use the <b>-o</b> option to
-specify the output file. The stacked format can be converted to Newick
-format using <a class="local sibling" href="mcxdump.html">mcxdump</a>. The output can be written to multiple files,
-one for each projected clustering, by using the <b>-prefix</b> option. By
-example, <b>-prefix</b> <b>P</b> leads to output in files named <tt>P1</tt>, <tt>P2</tt>,
-..<tt>PN</tt>, where <tt>N</tt> is the number of clusters in the input, <tt>P1</tt> is the
-most fine-grained ordered clustering, and <tt>PN</tt> is the coarsest clustering.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade item_leftalign nowrap" ><a name="opt-prefix"></a><b>-prefix</b> (<i><string></i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-o"></a><b>-o</b> (<i><fname></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-As decribed above.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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-<title>Work flows and protocols for mcl and friends</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmprotocols.ps"><b>clmprotocols</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#internal">Network representation</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#large">Loading large networks</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#formatconversion">Converting between formats</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#jobs">Using threading and job dispatching</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#blast">Clustering similarity graphs encoded in BLAST results</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#array">Clustering expression data</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#degree">Reducing node degrees in the graph</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">10.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">11.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clmprotocols — Work flows and protocols for mcl and friends</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-A guide to doing analysis with mcl and its helper programs.
-</p>
-
-<a name="internal"></a>
-<h2>Network representation</h2>
-<p style="margin-bottom:0" class="asd_par">
-The clustering program <b>mcl</b> expects the name of file as its first argument.
-If the <b>--abc</b> option is used, the file is assumed to adhere to a
-simple format where a network is specified edge by edge, one line and one
-edge at a time.
-Each line describes an edge as two labels and a numerical value, all
-separated by white space. The labels and the value respectively identify the
-two nodes and the edge weight. The format is called <span class="smallcaps">ABC</span>-format,
-where '<span class="smallcaps">A</span>' and '<span class="smallcaps">B</span>' represent the two labels and '<span class="smallcaps">C</span>' represents the
-edge weight. The latter is optional; if omitted the edge weight is set to one.
-If <span class="smallcaps">ABC</span>-format is used, the output is returned as a listing of clusters,
-each cluster given as a line of white-space separated labels.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-MCL can also utilize a second representation, which is a stringent and
-unambiguous format for both input and output.
-This is called <i>matrix format</i> and it is required when using other
-programs in the mcl suite, for example when comparing and analysing
-clusterings using <a class="local sibling" href="clm.html">clm</a> or when extracting and transforming
-networks using <a class="local sibling" href="mcx.html">mcx</a>.
-Native mode (matrix format) is entered simply by <i>not</i> specifying
-<b>--abc</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The recommended approach using <b>mcl</b> is to convert an external format to
-<span class="smallcaps">ABC</span>-format. The program <a class="local sibling" href="mcxload.html">mcxload</a> reads the latter and creates a
-native network file and a dictionary file that maps network nodes to
-labels. All applications in the MCL suite, including <b>mcl</b> itself, can read
-this native network file format. Label output can be obtained using
-<a class="local sibling" href="mcxdump.html">mcxdump</a>. The workflow is thus:
-</p>
-<div class="verbatim"> # External format has been converted to file data.abc (abc format)
-
- mcxload -abc data.abc --stream-mirror -write-tab data.tab -o data.mci
-
- mcl data.mci -I 1.4
- mcl data.mci -I 2
- mcl data.mci -I 4
-
- mcxdump -icl out.data.mci.I14 -tabr data.tab -o dump.data.mci.I14
- mcxdump -icl out.data.mci.I20 -tabr data.tab -o dump.data.mci.I20
- mcxdump -icl out.data.mci.I40 -tabr data.tab -o dump.data.mci.I40</div>
-<p style="margin-top:0em; margin-bottom:0em">
-In this example the cluster output is stored in native format and dumped to
-labels using mcxdump. The stored output can now be used to learn more about
-the clusterings. An example is the following, where <a class="local sibling" href="clm.html">clm</a> is applied
-in mode <b>dist</b> to gauge the distance between different clusterings.
-</p>
-<div class="verbatim"> clm dist --chain out.data.mci.I{14,20,40}</div>
-
-<a name="large"></a>
-<h2>Loading large networks</h2>
-<p style="margin-bottom:0" class="asd_par">
-If you deal with very large networks (say with hundreds of millions
-of edges), it is recommended to use binary format (cf <a class="local sibling" href="mcxio.html">mcxio</a>).
-This is simply achieved by adding <tt>--write-binary</tt> to the mcxload
-command line. The resulting file is no longer human-readable but
-will be faster to read by a factor between ten- or twenty-fold
-compared to standard <span class="smallcaps">MCL</span>-edge network format, and a factor around fifty-fold
-compared to label format.
-All <span class="smallcaps">MCL</span>-edge programs are able to read binary format, and speed
-of reading will be somewhere in the order of millions of edges
-per second, compared to, for example, roughly 100K edges
-per second for label format.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Memory usage for mcxload can be lowered
-by replacing the option <tt>--stream-mirror</tt> with <tt>-ri max</tt>.
-</p>
-
-<a name="formatconversion"></a>
-<h2>Converting between formats</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>Converting label format to tabular format</b><br>
-Label format, two or three (including weight) columns:
-</p>
-<div class="verbatim"> mcxload -abc data.abc --stream-mirror -write-tab data.tab -o data.mci
- mcxdump -imx data.mci -tab data.tab --dump-table</div>
-<p style="margin-top:0em; margin-bottom:0em">Simple Interaction File (SIF) format:</p>
-<div class="verbatim"> mcxload -sif data.sif --stream-mirror -write-tab data.tab -o data.mci
- mcxdump -imx data.mci -tab data.tab --dump-table</div>
-<p style="margin-top:0em; margin-bottom:0em">
-These two examples are very similar, and differ only in the way the input to <b>mcxload</b> is specified.
-</p>
-
-<a name="jobs"></a>
-<h2>Using threading and job dispatching</h2>
-<p style="margin-bottom:0" class="asd_par">
-The programs <a class="local sibling" href="mcxarray.html">mcxarray</a>, <a class="local sibling" href="mcxclcf.html">mcx clcf</a>, <a class="local sibling" href="mcxctty.html">mcx ctty</a>,
-<a class="local sibling" href="mcxdiameter.html">mcx diameter</a> and <a class="local sibling" href="clminfo2.html">clm info2</a> can all make use of both
-threading and job dispatching. The clustering program <a class="local sibling" href="mcl.html">mcl</a>
-can only use threading.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Instructing these programs to use threads is easy. It just requires
-supplying <b>-t</b> <b><num></b>, e.g. use <b>-t</b> <b>4</b> to generate four threads.
-It is only sensible to use <tt><num></tt> threads on a machine that has at least <tt><num></tt> CPUs.
-It is additionally recommended that a threaded program has exclusive access to those CPUs
-and does not have to contend with other jobs.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For the afore-mentioned programs it is additionally possible to split the computational
-load over multiple machines. If <tt><N></tt> machines are available then <tt><N></tt> jobs should
-be started. Each job should have an identical parameter <b>-J</b> <b>N</b> (e.g. <b>-J</b> <b>10</b>),
-and varying parameters <b>-j</b> <b>0</b>, <b>-j</b> <b>1</b>, ... <b>-j</b> <b>N-1</b> (e.g. <b>-j</b> <b>9</b>).
-It is possible to use threads in each individual job, but the number of threads should be
-identical across all jobs issued. Output should typically be directed using a convention
-such as <b>-o</b> <b>out.0</b>, <b>-o</b> <b>out.1</b>, ... <b>-o</b> <b>out.9</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-After all jobs have finished the outputs must be combined to form the final answer.
-The manner in which this is done is dependent on the program used.
-With the example output above this would be done as follows. It can be seen
-that <a class="local sibling" href="clminfo2.html">clm info2</a> is not yet supported by <a class="local sibling" href="mcxcollect.html">mcx collect</a> and requires somewhat
-idiosyncratic processing.
-</p>
-<div class="verbatim"> # mcx diameter:
- mcx collect --add-column -o out.diameter out.{0,1,2,3,4,5,6,7,8,9}
-
- # mcx ctty:
- mcx collect --add-column -o out.ctty out.{0,1,2,3,4,5,6,7,8,9}
-
- # mcx clcf:
- mcx collect --add-column -o out.clcf out.{0,1,2,3,4,5,6,7,8,9}
-
- # mcxarray:
- mcx collect --add-matrix -o out.ctty out.{0,1,2,3,4,5,6,7,8,9}
-
- # clm info2:
- clxdo add_table out.{0,1,2,3,4,5,6,7,8,9} > out.info2</div>
-
-<a name="blast"></a>
-<h2>Clustering similarity graphs encoded in BLAST results</h2>
-<p style="margin-bottom:0" class="asd_par">
-A specific instance of the workflow above is the clustering of proteins based on
-their sequence similarities. In the most typical scenario the external
-format is BLAST output, which needs to be transformed to <span class="smallcaps">ABC</span> format.
-In the examples below the input is in columnar blast format
-obtained with the blast -m8 option.
-It requires a version of <b>mcl</b> at least as recent as <tt>09-061</tt>.
-First we create an <span class="smallcaps">ABC</span>-formatted file using the external columnar BLAST
-format, which is assumed to be in a file called <tt>seq.cblast</tt>.
-</p>
-<div class="verbatim"> cut -f 1,2,11 seq.cblast > seq.abc</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The columnar format in the file <tt>seq.cblast</tt> has, for a given BLAST hit,
-the sequence labels in the first two columns and the asssociated E-value in
-column 11. It is parsed by the standard UNIX cut(1) utility. The format
-must have been created with the BLAST -m8 option so that no comment lines
-are present. Alternatively these can be filtered out using grep.
-</p>
-<p style="margin-top:0em; margin-bottom:0em">
-The newly created <tt>seq.abc</tt> file is loaded by <a class="local sibling" href="mcxload.html">mcxload</a>,
-which writes both a network file <tt>seq.mci</tt> and a dictionary
-file <tt>seq.tab</tt>.
-</p>
-<div class="verbatim"> mcxload -abc seq.abc --stream-mirror --stream-neg-log10 -stream-tf 'ceil(200)'
- -o seq.mci -write-tab seq.tab</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The <tt>--stream-mirror</tt> option ensures that the resulting network will be
-undirected, as recommended when using <b>mcl</b>. Omitting this option would
-result in a directed network as BLAST E-values generally differ between two
-sequences. The default course of action for <a class="local sibling" href="mcxload.html">mcxload</a> is to use the
-best value found between a pair of labels. The next option,
-<tt>--abc-neg-log10</tt> tranforms the numerical values in the input (the BLAST
-E-values) by taking the logarithm in base 10 and subsequently negating the
-sign. Finally, the transformed values are capped so that any E-value below
-1e-200 is set to a maximum allowed edge weight of 200.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-To obtain clusterings from <tt>seq.mci</tt> and <tt>seq.tab</tt> one has two
-choices. The first is to generate an abstract clustering representation
-and from that obtain the label output, as follows.
-Below the <b>-o</b> option is not used, so mcl will create meaningful and
-unique output names by itself. The default way of doing this is to preprend
-the prefix <tt>out.</tt> and to append a suffix encoding the inflation value
-used, with inflation encoded using two digits of precision and the decimal
-separator removed.
-</p>
-<div class="verbatim"> mcl seq.mci -I 1.4
- mcl seq.mci -I 2
- mcl seq.mci -I 4
- mcl seq.mci -I 6
-
- mcxdump -icl out.seq.mci.I14 -tabr seq.tab -o dump.seq.mci.I14
- mcxdump -icl out.seq.mci.I20 -tabr seq.tab -o dump.seq.mci.I20
- mcxdump -icl out.seq.mci.I40 -tabr seq.tab -o dump.seq.mci.I40
- mcxdump -icl out.seq.mci.I60 -tabr seq.tab -o dump.seq.mci.I60</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Now the file <tt>out.seq.tab.I14</tt> and its associates can be used for example
-to compute the distances between the encoded clusterings with
-<b>clm dist</b>, to compute a set of strictly reconciled nested clusterings
-with <b>clm order</b>, or to compute an efficiency criterion with
-<b>clm info</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Alternatively, label output can be obtained directly from <b>mcl</b>
-as follows.</p>
-<div class="verbatim"> mcl seq.mci -I 1.4 -use-tab seq.tab
- mcl seq.mci -I 2 -use-tab seq.tab
- mcl seq.mci -I 4 -use-tab seq.tab
- mcl seq.mci -I 6 -use-tab seq.tab</div>
-
-<a name="array"></a>
-<h2>Clustering expression data</h2>
-<p style="margin-bottom:0" class="asd_par">
-The clustering of expression data constitutes another workflow. In this case the
-external format usually is a tabular file format containing labels for genes
-or probes and numerical values measuring the expression values or fold
-changes across a series of conditions or experiments. Such tabular files can
-be processed by <a class="local sibling" href="mcxarray.html">mcxarray</a>, which comes installed with <b>mcl</b>. The
-program computes correlations (either Pearson or Spearmann) between genes,
-and creates an edge between genes if their correlation exceeds the specified
-cutoff. From this <a class="local sibling" href="mcxarray.html">mcxarray</a> creates both a network file and a
-dictionary file. In the example below, the file <tt>expr.data</tt> is
-in tabular format with one row of column headers (e.g. tags for
-experiments) and one column of row identifiers (e.g. probe or gene identifiers).
-</p>
-<div class="verbatim"> mcxarray -data expr.data -skipr 1 -skipc 1 -o expr.mci -write-tab expr.tab --pearson -co 0.7 -tf 'abs(),add(-0.7)'
- </div>
-<p style="margin-top:0em; margin-bottom:0em">
-This uses the Pearson correlation, ignoring values below 0.7.
-The remaining values in the interval <tt>[0.7-1]</tt> are remapped to the interval
-<tt>[0-0.3]</tt>. This is recommended so that the edge weights will have
-increased contrast between them, as <b>mcl</b> is affected by relative differences
-(ratios) between edge weights rather than absolute differences. To illustrate
-this, values 0.75 and 0.95 are mapped to 0.05 and 0.25, with respective
-ratios 0.79 and 0.25.
-The network file <tt>expr.mci</tt> and the dictionary file <tt>expr.tab</tt> can
-now be used as before.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible to investigate the effect of the correlation cutoff as follows.
-First a network is generated at a very low threshold, and this network
-is analysed using <b>mcxquery</b>.
-</p>
-<div class="verbatim"> mcxarray -data expr.data -skipr 1 -skipc 1 -o expr20.mcx --write-binary --pearson -co 0.2 -tf 'abs()'
- mcx query -imx expr20.mcx --vary-correlation
- </div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output is in a tabular format describing the properties of the network
-at increasing correlation thresholds. Examples are the size of the biggest
-component, the number of orphan nodes (not connected to any other node), and
-the mean and median node degrees.
-A good way to choose the cutoff is to balance the number of singletons
-and the median node degree. Both should preferably not be too high.
-For example the number of orphan nodes should be
-less than ten percent of the total number of nodes,
-and the median node degree should be at most one hundred neighbours.
-</p>
-
-<a name="degree"></a>
-<h2>Reducing node degrees in the graph</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-A good way to lower node degrees in a network is to require that
-an edge is among the best <i>k</i> edges (those of highest weight) for
-<i>both</i> nodes incident to the edge, for some value of <i>k</i>. This is
-achieved by using <tt>knn(k)</tt> in the argument to the <b>-tf</b> option to
-mcl or <b>mcx alter</b>.
-To give an example, a graph was formed on translations in Ensembl release 57 on 2.6M nodes.
-The similarities were obtained from BLAST scores,
-leading to a graph with a total edge count of 300M, with
-best-connected nodes of degree respectively
-11148, 9083, 9070, 9019 and 8988, and with mean node degree 233.
-These degrees are unreasonable.
-The graph was subjected to <b>mcx query</b> to investigate the effect of
-varying k-NN parameters. A good heuristic is to choose a value
-that does not significantly change the number of singletons in the input graph.
-In the example it meant that <b>-tf</b> <b>'knn(160)'</b> was feasible, leading
-to a mean node degree of 98.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-A second approach to reduce node degrees is to employ the <b>-ceil-nb</b> option.
-This ranks nodes by node degree, highest first. Nodes are considered
-in order of rank, and edges of low weight are removed from the graph until
-a node satisfies the node degree threshold specified by <b>-ceil-nb</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Stijn van Dongen.</p>
-</body>
-</html>
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-<title>Work flows and protocols for mcl and friends</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmprotocols2.ps"><b>clmprotocols</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#toc">TOC</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#faq">FAQ</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#internal">Network representation</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#large">Loading large networks</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#formatconversion">Converting between formats</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#blast">Clustering similarity graphs encoded in BLAST results</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#array">Clustering expression data</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">10.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#degree">Reducing node degrees in the graph</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">11.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">12.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-</div>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#toc">TOC</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#faq">FAQ</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#internal">Network representation</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#large">Loading large networks</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#formatconversion">Converting between formats</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#blast">Clustering similarity graphs encoded in BLAST results</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#array">Clustering expression data</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">10.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#degree">Reducing node degrees in the graph</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">11.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">12.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clmprotocols — Work flows and protocols for mcl and friends</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-A guide to doing analysis with mcl and its helper programs.
-</p>
-
-<a name="toc"></a>
-<h2>TOC</h2>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-general2"></a><a class="quiet" href="#general2"><b>1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#general2"><b>General pardon</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.1"></a> <a class="intern" href="#faq1.1"><b>1.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.1"><b>For whom is mcl and for whom is this FAQ?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.2"></a> <a class="intern" href="#faq1.2"><b>1.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.2"><b>For whom is mcl and for whom is this FAQ?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-general"></a><a class="quiet" href="#general"><b>2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#general"><b>General questions</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq2.1"></a> <a class="intern" href="#faq2.1"><b>2.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq2.1"><b>For whom is mcl and for whom is this FAQ?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq2.2"></a> <a class="intern" href="#faq2.2"><b>2.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq2.2"><b>For whom is mcl and for whom is this FAQ?</b></a>
-</div>
-</div>
-<br><br>
-
-<a name="faq"></a>
-<h2>FAQ</h2>
-
-<div align=center>
-<h3><a name="general2"></a><a class="quiet" href="#toc-general2">1</a><br>General pardon
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.1"></a> <a class="quiet" href="#toc-general2">1.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For whom is mcl and for whom is this FAQ?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For everybody with an appetite for graph clustering.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.2"></a> <a class="quiet" href="#toc-general2">1.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For whom is mcl and for whom is this FAQ?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For everybody with an appetite for graph clustering.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="general"></a><a class="quiet" href="#toc-general">2</a><br>General questions
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq2.1"></a> <a class="quiet" href="#toc-general">2.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For whom is mcl and for whom is this FAQ?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For everybody with an appetite for graph clustering.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq2.2"></a> <a class="quiet" href="#toc-general">2.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For whom is mcl and for whom is this FAQ?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For everybody with an appetite for graph clustering.</p>
-</div>
-</div>
-
-<a name="internal"></a>
-<h2>Network representation</h2>
-<p style="margin-bottom:0" class="asd_par">
-The clustering program <b>mcl</b> expects the name of file as its first argument.
-If the <b>--abc</b> option is used, the file is assumed to adhere to a
-simple format where a network is specified edge by edge, one line and one
-edge at a time.
-Each line describes an edge as two labels and a numerical value, all
-separated by white space. The labels and the value respectively identify the
-two nodes and the edge weight. The format is called <span class="smallcaps">ABC</span>-format,
-where '<span class="smallcaps">A</span>' and '<span class="smallcaps">B</span>' represent the two labels and '<span class="smallcaps">C</span>' represents the
-edge weight. The latter is optional; if omitted the edge weight is set to one.
-If <span class="smallcaps">ABC</span>-format is used, the output is returned as a listing of clusters,
-each cluster given as a line of white-space separated labels.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-MCL can also utilize a second representation, which is a stringent and
-unambiguous format for both input and output.
-This is called <i>matrix format</i> and it is required when using other
-programs in the mcl suite, for example when comparing and analysing
-clusterings using <a class="local sibling" href="clm.html">clm</a> or when extracting and transforming
-networks using <a class="local sibling" href="mcx.html">mcx</a>.
-Native mode (matrix format) is entered simply by <i>not</i> specifying
-<b>--abc</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The recommended approach using <b>mcl</b> is to convert an external format to
-<span class="smallcaps">ABC</span>-format. The program <a class="local sibling" href="mcxload.html">mcxload</a> reads the latter and creates a
-native network file and a dictionary file that maps network nodes to
-labels. All applications in the MCL suite, including <b>mcl</b> itself, can read
-this native network file format. Label output can be obtained using
-<a class="local sibling" href="mcxdump.html">mcxdump</a>. The workflow is thus:
-</p>
-<div class="verbatim"> # External format has been converted to file data.abc (abc format)
-
- mcxload -abc data.abc --stream-mirror -write-tab data.tab -o data.mci
-
- mcl data.mci -I 1.4
- mcl data.mci -I 2
- mcl data.mci -I 4
-
- mcxdump -icl out.data.mci.I14 -tabr data.tab -o dump.data.mci.I14
- mcxdump -icl out.data.mci.I20 -tabr data.tab -o dump.data.mci.I20
- mcxdump -icl out.data.mci.I40 -tabr data.tab -o dump.data.mci.I40</div>
-<p style="margin-top:0em; margin-bottom:0em">
-In this example the cluster output is stored in native format and dumped to
-labels using mcxdump. The stored output can now be used to learn more about
-the clusterings. An example is the following, where <a class="local sibling" href="clm.html">clm</a> is applied
-in mode <b>dist</b> to gauge the distance between different clusterings.
-</p>
-<div class="verbatim"> clm dist --chain out.data.mci.I{14,20,40}</div>
-
-<a name="large"></a>
-<h2>Loading large networks</h2>
-<p style="margin-bottom:0" class="asd_par">
-If you deal with very large networks (say with hundreds of millions
-of edges), it is recommended to use binary format (cf <a class="local sibling" href="mcxio.html">mcxio</a>).
-This is simply achieved by adding <tt>--write-binary</tt> to the mcxload
-command line. The resulting file is no longer human-readable but
-will be faster to read by a factor between ten- or twenty-fold
-compared to standard <span class="smallcaps">MCL</span>-edge network format, and a factor around fifty-fold
-compared to label format.
-All <span class="smallcaps">MCL</span>-edge programs are able to read binary format, and speed
-of reading will be somewhere in the order of millions of edges
-per second, compared to, for example, roughly 100K edges
-per second for label format.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Memory usage for mcxload can be lowered
-by replacing the option <tt>--stream-mirror</tt> with <tt>-ri max</tt>.
-</p>
-
-<a name="formatconversion"></a>
-<h2>Converting between formats</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>Converting label format to tabular format</b><br>
-Label format, two or three (including weight) columns:
-</p>
-<div class="verbatim"> mcxload -abc data.abc --stream-mirror -write-tab data.tab -o data.mci
- mcxdump -imx data.mci -tab data.tab --dump-table</div>
-<p style="margin-top:0em; margin-bottom:0em">Simple Interaction File (SIF) format:</p>
-<div class="verbatim"> mcxload -sif data.sif --stream-mirror -write-tab data.tab -o data.mci
- mcxdump -imx data.mci -tab data.tab --dump-table</div>
-<p style="margin-top:0em; margin-bottom:0em">
-It can be noted that these two examples are very similar, and differ
-only in the way the input to <b>mcxload</b> is specified.
-</p>
-
-<a name="blast"></a>
-<h2>Clustering similarity graphs encoded in BLAST results</h2>
-<p style="margin-bottom:0" class="asd_par">
-A specific instance of the workflow above is the clustering of proteins based on
-their sequence similarities. In the most typical scenario the external
-format is BLAST output, which needs to be transformed to <span class="smallcaps">ABC</span> format.
-In the examples below the input is in columnar blast format
-obtained with the blast -m8 option.
-It requires a version of <b>mcl</b> at least as recent as <tt>09-061</tt>.
-First we create an <span class="smallcaps">ABC</span>-formatted file using the external columnar BLAST
-format, which is assumed to be in a file called <tt>seq.cblast</tt>.
-</p>
-<div class="verbatim"> cut -f 1,2,11 seq.cblast > seq.abc</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The columnar format in the file <tt>seq.cblast</tt> has, for a given BLAST hit,
-the sequence labels in the first two columns and the asssociated E-value in
-column 11. It is parsed by the standard UNIX cut(1) utility. The format
-must have been created with the BLAST -m8 option so that no comment lines
-are present. Alternatively these can be filtered out using grep.
-</p>
-<p style="margin-top:0em; margin-bottom:0em">
-The newly created <tt>seq.abc</tt> file is loaded by <a class="local sibling" href="mcxload.html">mcxload</a>,
-which writes both a network file <tt>seq.mci</tt> and a dictionary
-file <tt>seq.tab</tt>.
-</p>
-<div class="verbatim"> mcxload -abc seq.abc --stream-mirror --stream-neg-log10 -stream-tf 'ceil(200)'
- -o seq.mci -write-tab seq.tab</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The <tt>--stream-mirror</tt> option ensures that the resulting network will be
-undirected, as recommended when using <b>mcl</b>. Omitting this option would
-result in a directed network as BLAST E-values generally differ between two
-sequences. The default course of action for <a class="local sibling" href="mcxload.html">mcxload</a> is to use the
-best value found between a pair of labels. The next option,
-<tt>--abc-neg-log10</tt> tranforms the numerical values in the input (the BLAST
-E-values) by taking the logarithm in base 10 and subsequently negating the
-sign. Finally, the transformed values are capped so that any E-value below
-1e-200 is set to a maximum allowed edge weight of 200.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-To obtain clusterings from <tt>seq.mci</tt> and <tt>seq.tab</tt> one has two
-choices. The first is to generate an abstract clustering representation
-and from that obtain the label output, as follows.
-Below the <b>-o</b> option is not used, so mcl will create meaningful and
-unique output names by itself. The default way of doing this is to preprend
-the prefix <tt>out.</tt> and to append a suffix encoding the inflation value
-used, with inflation encoded using two digits of precision and the decimal
-separator removed.
-</p>
-<div class="verbatim"> mcl seq.mci -I 1.4
- mcl seq.mci -I 2
- mcl seq.mci -I 4
- mcl seq.mci -I 6
-
- mcxdump -icl out.seq.mci.I14 -tabr seq.tab -o dump.seq.mci.I14
- mcxdump -icl out.seq.mci.I20 -tabr seq.tab -o dump.seq.mci.I20
- mcxdump -icl out.seq.mci.I40 -tabr seq.tab -o dump.seq.mci.I40
- mcxdump -icl out.seq.mci.I60 -tabr seq.tab -o dump.seq.mci.I60</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Now the file <tt>out.seq.tab.I14</tt> and its associates can be used for example
-to compute the distances between the encoded clusterings with
-<b>clm dist</b>, to compute a set of strictly reconciled nested clusterings
-with <b>clm order</b>, or to compute an efficiency criterion with
-<b>clm info</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Alternatively, label output can be obtained directly from <b>mcl</b>
-as follows.</p>
-<div class="verbatim"> mcl seq.mci -I 1.4 -use-tab seq.tab
- mcl seq.mci -I 2 -use-tab seq.tab
- mcl seq.mci -I 4 -use-tab seq.tab
- mcl seq.mci -I 6 -use-tab seq.tab</div>
-
-<a name="array"></a>
-<h2>Clustering expression data</h2>
-<p style="margin-bottom:0" class="asd_par">
-The clustering of expression data constitutes another workflow. In this case the
-external format usually is a tabular file format containing labels for genes
-or probes and numerical values measuring the expression values or fold
-changes across a series of conditions or experiments. Such tabular files can
-be processed by <a class="local sibling" href="mcxarray.html">mcxarray</a>, which comes installed with <b>mcl</b>. The
-program computes correlations (either Pearson or Spearmann) between genes,
-and creates an edge between genes if their correlation exceeds the specified
-cutoff. From this <a class="local sibling" href="mcxarray.html">mcxarray</a> creates both a network file and a
-dictionary file. In the example below, the file <tt>expr.data</tt> is
-in tabular format with one row of column headers (e.g. tags for
-experiments) and one column of row identifiers (e.g. probe or gene identifiers).
-</p>
-<div class="verbatim"> mcxarray -data expr.data -skipr 1 -skipc 1 -o expr.mci -write-tab expr.tab --pearson -co 0.7 -tf 'abs(),add(-0.7)'
- </div>
-<p style="margin-top:0em; margin-bottom:0em">
-This uses the Pearson correlation, ignoring values below 0.7.
-The remaining values in the interval <tt>[0.7-1]</tt> are remapped to the interval
-<tt>[0-0.3]</tt>. This is recommended so that the edge weights will have
-increased contrast between them, as <b>mcl</b> is affected by relative differences
-(ratios) between edge weights rather than absolute differences. To illustrate
-this, values 0.75 and 0.95 are mapped to 0.05 and 0.25, with respective
-ratios 0.79 and 0.25.
-The network file <tt>expr.mci</tt> and the dictionary file <tt>expr.tab</tt> can
-now be used as before.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible to investigate the effect of the correlation cutoff as follows.
-First a network is generated at a very low threshold, and this network
-is analysed using <b>mcxquery</b>.
-</p>
-<div class="verbatim"> mcxarray -data expr.data -skipr 1 -skipc 1 -o expr20.mcx --write-binary --pearson -co 0.2 -tf 'abs()'
- mcx query -imx expr20.mcx --vary-correlation
- </div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output is in a tabular format describing the properties of the network
-at increasing correlation thresholds. Examples are the size of the biggest
-component, the number of orphan nodes (not connected to any other node), and
-the mean and median node degrees.
-A good way to choose the cutoff is to balance the number of singletons
-and the median node degree. Both should preferably not be too high.
-For example the number of orphan nodes should be
-less than ten percent of the total number of nodes,
-and the median node degree should be at most one hundred neighbours.
-</p>
-
-<a name="degree"></a>
-<h2>Reducing node degrees in the graph</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-A good way to lower node degrees in a network is to require that
-an edge is among the best <i>k</i> edges (those of highest weight) for
-<i>both</i> nodes incident to the edge, for some value of <i>k</i>. This is
-achieved by using <tt>knn(k)</tt> in the argument to the <b>-tf</b> option to
-mcl or <b>mcx alter</b>.
-To give an example, a graph was formed on translations in Ensembl release 57 on 2.6M nodes.
-The similarities were obtained from BLAST scores,
-leading to a graph with a total edge count of 300M, with
-best-connected nodes of degree respectively
-11148, 9083, 9070, 9019 and 8988, and with mean node degree 233.
-These degrees are unreasonable.
-The graph was subjected to <b>mcx query</b> to investigate the effect of
-varying k-NN parameters. A good heuristic is to choose a value
-that does not significantly change the number of singletons in the input graph.
-In the example it meant that <b>-tf</b> <b>'knn(160)'</b> was feasible, leading
-to a mean node degree of 98.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-A second approach to reduce node degrees is to employ the <b>-ceil-nb</b> option.
-This ranks nodes by node degree, highest first. Nodes are considered
-in order of rank, and edges of low weight are removed from the graph until
-a node satisfies the node degree threshold specified by <b>-ceil-nb</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Stijn van Dongen.</p>
-</body>
-</html>
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diff --git a/doc/clmresidue.1 b/doc/clmresidue.1
deleted file mode 100644
index f574186..0000000
--- a/doc/clmresidue.1
+++ /dev/null
@@ -1,96 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm residue" 1 "16 May 2014" "clm residue 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-clm residue \- extend clustering of subgraph to clustering of graph\&.
-
-clmresidue is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIresidue\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm residue\fP
-\fB-icl\fP fname (\fIinput clustering\fP)
-\fB-imx\fP fname (\fIinput graph\fP)
-\fB[-rpm\fP fname (\fIresidue projection matrix\fP)\fB]\fP
-\fB[-o\fP fname (\fIoutput clustering file\fP)\fB]\fP
-.SH DESCRIPTION
-
-The cluster file presumably contains a clustering of a subgraph of the
-graph\ \&\fCG\fP contained by the matrix file, implying that the row domain of
-that clustering is a subset of the node domain of the graph\&. \fBclm residue\fP will
-compute a simple upwards projection of that clustering, resulting in a
-clustering of\ \&\fCG\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP fname (\fIinput graph\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-icl\fP fname (\fIinput clustering\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-rpm\fP fname (\fIresidue projection matrix\fP)"
-\&
-.br
-The name for the file in which the residue projection matrix is stored\&.
-It contains for each node and for each cluster in the input clustering
-the combined weight of the (edges to the) neighbours of that node
-in that cluster\&.
-The default output file name is \fCout\&.rpm\fP\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput clustering file\fP)"
-\&
-.br
-The name for the file in which the majority vote projection clustering
-is stored\&. Aka the majority vote projection clustering storage file name\&.
-
-This embodies a very crude approach to distributing the missing nodes in the
-input clustering onto that same cluster\&. For each node, the cluster is
-taken for which the residue projection is the largest (see above)\&. The
-residue (i\&.e\&. the set of missing nodes) is initially viewed as a cluster;
-the set of nodes for which the projection is largest for the residue itself
-will form a new cluster, if it is not empty\&.
-
-By default output is sent to STDOUT\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmresidue.html b/doc/clmresidue.html
deleted file mode 100644
index 15e6df2..0000000
--- a/doc/clmresidue.html
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@@ -1,196 +0,0 @@
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-{ text-align: justify;
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-<title>The clm residue manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmresidue.ps"><b>clm residue</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm residue — extend clustering of subgraph to clustering of graph.</p>
-<p style="margin-bottom:0" class="asd_par">clmresidue is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>residue</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm residue</b>
-<a class="intern" href="#opt-icl"><b>-icl</b> fname (<i>input clustering</i>)</a>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input graph</i>)</a>
-<a class="intern" href="#opt-rpm"><b>[-rpm</b> fname (<i>residue projection matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output clustering file</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The cluster file presumably contains a clustering of a subgraph of the
-graph <tt>G</tt> contained by the matrix file, implying that the row domain of
-that clustering is a subset of the node domain of the graph. <b>clm residue</b> will
-compute a simple upwards projection of that clustering, resulting in a
-clustering of <tt>G</tt>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input graph</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> fname (<i>input clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-rpm"></a><b>-rpm</b> fname (<i>residue projection matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name for the file in which the residue projection matrix is stored.
-It contains for each node and for each cluster in the input clustering
-the combined weight of the (edges to the) neighbours of that node
-in that cluster.
-</p>
-<p style="margin-top:0em; margin-bottom:0em">
-The default output file name is <tt>out.rpm</tt>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output clustering file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name for the file in which the majority vote projection clustering
-is stored. Aka the majority vote projection clustering storage file name.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This embodies a very crude approach to distributing the missing nodes in the
-input clustering onto that same cluster. For each node, the cluster is
-taken for which the residue projection is the largest (see above). The
-residue (i.e. the set of missing nodes) is initially viewed as a cluster;
-the set of nodes for which the projection is largest for the residue itself
-will form a new cluster, if it is not empty.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-By default output is sent to STDOUT.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/clmvol.1 b/doc/clmvol.1
deleted file mode 100644
index f2813e3..0000000
--- a/doc/clmvol.1
+++ /dev/null
@@ -1,81 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "clm vol" 1 "16 May 2014" "clm vol 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
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-.am SH
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-..
-.SH NAME
-clm vol \- compute volatile nodes from a set of clusterings
-
-clmvol is not in actual fact a program\&. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode \fIvol\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
-in all \fBclm\fP modes\&. They are described
-in the \fBclm\fP manual page\&.
-.SH SYNOPSIS
-
-\fBclm vol\fP
-\fB[-fraction\fP num (\fInff factor\fP)\fB]\fP
-\fB[-o\fP fname (\fIoutput file\fP)\fB]\fP
-<cl file>+
-.SH DESCRIPTION
-
-\fBclm vol\fP computes a score for each node, which at a minimum is equal to one\&.
-The output is in the form of a matrix containing a single column\&. The score
-correlates with what is deemed to be volatile behaviour\&. For all pairs of
-clusterings the set of all intersections is computed, and these are
-considered in turn\&.
-An intersection is deemed to be volatile if the size of the intersection is
-less than half the size of the smallest of the two clusters\&. In that case,
-for each node in the intersection its volatility score is incremented by one
-over the size of the intersection\&.
-The size comparison can be made more stringent by increasing the
-\fB-fraction\fP\ \&\fI<frac>\fP option, which is by default set to \fC0\&.5\fP\&.
-Volatility occurs if the size of the intersection is less than
-\fB<frac>\fP times the size of the smallest cluster\&. If the
-\fB-fraction\fP value is increased all the way up to 1\&.0, the implication
-is that an intersection is considered volatile unless one of the two
-clusteres considered is a subset of the other\&.
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-fraction\fP num (\fInff factor\fP)"
-\&
-.br
-See the discussion at \fBDESCRIPTION\fP\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
-\&
-.br
-.in -2m
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/clmvol.html b/doc/clmvol.html
deleted file mode 100644
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--- a/doc/clmvol.html
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-<title>The clm vol manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="clmvol.ps"><b>clm vol</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-clm vol — compute volatile nodes from a set of clusterings</p>
-<p style="margin-bottom:0" class="asd_par">clmvol is not in actual fact a program. This manual
-page documents the behaviour and options of the clm program when
-invoked in mode <i>vol</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
-in all <b>clm</b> modes. They are described
-in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm vol</b>
-<a class="intern" href="#opt-fraction"><b>[-fraction</b> num (<i>nff factor</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file</i>)<b>]</b></a>
-<cl file>+
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>clm vol</b> computes a score for each node, which at a minimum is equal to one.
-The output is in the form of a matrix containing a single column. The score
-correlates with what is deemed to be volatile behaviour. For all pairs of
-clusterings the set of all intersections is computed, and these are
-considered in turn.
-An intersection is deemed to be volatile if the size of the intersection is
-less than half the size of the smallest of the two clusters. In that case,
-for each node in the intersection its volatility score is incremented by one
-over the size of the intersection.
-The size comparison can be made more stringent by increasing the
-<b>-fraction</b> <i><frac></i> option, which is by default set to <tt>0.5</tt>.
-Volatility occurs if the size of the intersection is less than
-<b><frac></b> times the size of the smallest cluster. If the
-<b>-fraction</b> value is increased all the way up to 1.0, the implication
-is that an intersection is considered volatile unless one of the two
-clusteres considered is a subset of the other.
-</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-fraction"></a><b>-fraction</b> num (<i>nff factor</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">See the discussion at <a class="intern" href="#description">DESCRIPTION</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/distindex.html b/doc/distindex.html
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-
- <html>
-
- <head>
- <title>MCL manuals</title>
- <style type="text/css">
- body
- { text-align: justify;
- color: #001111;
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- margin-right: 8%;
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- h2 { margin-top:2em; }
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- <body>
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-
-
- <hr noshade size=1>
- <h1> MCL user manuals </h1>
- <h3> Distribution index 14-137 </h3>
- <hr noshade size=1>
-
-
-
-
-
-
-
-
-
- <h3 style="margin-top:2em">Generic stuff</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>mcl</b> - the mcl manual page</td>
- <td><a href="mcl.html">html</a></td>
- <td><a href="mcl.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mclfaq</b> - the mcl FAQ</td>
- <td><a href="mclfaq.html">html</a></td>
- <td><a href="mclfaq.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxio</b> - the mcl matrix format specification</td>
- <td><a href="mcxio.html">html</a></td>
- <td><a href="mcxio.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mclpipeline</b> - generic pipeline (parsing/matrix creation/clustering/display)</td>
- <td><a href="mclpipeline.html">html</a></td>
- <td><a href="mclpipeline.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcx</b> - interface to basic matrix operations</td>
- <td><a href="mcx.html">html</a></td>
- <td><a href="mcx.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
- <td><a href="mcxassemble.html">html</a></td>
- <td><a href="mcxassemble.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxdump</b> - dump matrices, optionally map indices to labels</td>
- <td><a href="mcxdump.html">html</a></td>
- <td><a href="mcxdump.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxarray</b> - transform array data to MCL matrices</td>
- <td><a href="mcxarray.html">html</a></td>
- <td><a href="mcxarray.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxconvert</b> - convert between ascii/binary storage types</td>
- <td><a href="mcxconvert.html">html</a></td>
- <td><a href="mcxconvert.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Dealing with clustering results</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>clmformat</b> - display clusterings in browsable format</td>
- <td><a href="clmformat.html">html</a></td>
- <td><a href="clmformat.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmdist</b> - compute distances between clusterings</td>
- <td><a href="clmdist.html">html</a></td>
- <td><a href="clmdist.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clminfo</b> - performance measures for clusterings</td>
- <td><a href="clminfo.html">html</a></td>
- <td><a href="clminfo.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmmeet</b> - compute intersection of clusterings</td>
- <td><a href="clmmeet.html">html</a></td>
- <td><a href="clmmeet.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmmate</b> - compute best matches between two clusterings</td>
- <td><a href="clmmate.html">html</a></td>
- <td><a href="clmmate.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmimac</b> - Interpret Matrices (c.q. MCL iterands) As Clusterings</td>
- <td><a href="clmimac.html">html</a></td>
- <td><a href="clmimac.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmresidue</b> - extend subgraph clusterings onto encompassing graph</td>
- <td><a href="clmresidue.html">html</a></td>
- <td><a href="clmresidue.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmorder</b> - reorder indices to represent blocks from different clusterings</td>
- <td><a href="clmorder.html">html</a></td>
- <td><a href="clmorder.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmclose</b> - fetch connected components from graphs or subgraphs</td>
- <td><a href="clmclose.html">html</a></td>
- <td><a href="clmclose.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Dealing with matrices</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>mcxio</b> - the mcl matrix format specification</td>
- <td><a href="mcxio.html">html</a></td>
- <td><a href="mcxio.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcx</b> - interface to basic matrix operations</td>
- <td><a href="mcx.html">html</a></td>
- <td><a href="mcx.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxsubs</b> - extract submatrices by specifiying sets of nodes and clusters</td>
- <td><a href="mcxsubs.html">html</a></td>
- <td><a href="mcxsubs.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxmap</b> - remap matrix indices / relabel graph nodes</td>
- <td><a href="mcxmap.html">html</a></td>
- <td><a href="mcxmap.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
- <td><a href="mcxassemble.html">html</a></td>
- <td><a href="mcxassemble.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Application specific parsers and wrappers</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
- <tr>
- <th colspan="3">
- <b>BLAST package</b> - Install with <b>--enable-blast</b>
- </th>
- </tr>
-
- <tr>
- <td><b>mclblastline</b> - pipeline for clustering from blast files</td>
- <td><a href="mclblastline.html">html</a></td>
- <td><a href="mclblastline.ps">ps</a></td>
- </tr>
- <tr>
- <td><b>mcxdeblast</b> - prepare input from blast files</td>
- <td><a href="mcxdeblast.html">html</a></td>
- <td><a href="mcxdeblast.ps">ps</a></td>
- </tr>
-</table>
-
-
-</body>
-</html>
-
-
-
-
diff --git a/doc/index.html b/doc/index.html
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--- a/doc/index.html
+++ /dev/null
@@ -1,199 +0,0 @@
-
- <html>
-
- <head>
- <title>MCL manuals</title>
- <style type="text/css">
- body
- { text-align: justify;
- color: #001111;
- background: white;
- margin-left: 8%;
- margin-right: 8%;
- }
- h3 { margin-top:1em; }
- h2 { margin-top:2em; }
- </style>
- </head>
-
- <body>
-
-
-
- <hr noshade size=1>
- <h1> MCL user manuals </h1>
- <h3> Installation index 14-137 </h3>
- <hr noshade size=1>
-
-
-
-
-
-
-
-
-
- <h3 style="margin-top:2em">Generic stuff</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>mcl</b> - the mcl manual page</td>
- <td><a href="mcl.html">html</a></td>
- <td><a href="mcl.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mclfaq</b> - the mcl FAQ</td>
- <td><a href="mclfaq.html">html</a></td>
- <td><a href="mclfaq.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxio</b> - the mcl matrix format specification</td>
- <td><a href="mcxio.html">html</a></td>
- <td><a href="mcxio.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mclpipeline</b> - generic pipeline (parsing/matrix creation/clustering/display)</td>
- <td><a href="mclpipeline.html">html</a></td>
- <td><a href="mclpipeline.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcx</b> - interface to basic matrix operations</td>
- <td><a href="mcx.html">html</a></td>
- <td><a href="mcx.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
- <td><a href="mcxassemble.html">html</a></td>
- <td><a href="mcxassemble.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxdump</b> - dump matrices, optionally map indices to labels</td>
- <td><a href="mcxdump.html">html</a></td>
- <td><a href="mcxdump.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxarray</b> - transform array data to MCL matrices</td>
- <td><a href="mcxarray.html">html</a></td>
- <td><a href="mcxarray.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxconvert</b> - convert between ascii/binary storage types</td>
- <td><a href="mcxconvert.html">html</a></td>
- <td><a href="mcxconvert.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Dealing with clustering results</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>clmformat</b> - display clusterings in browsable format</td>
- <td><a href="clmformat.html">html</a></td>
- <td><a href="clmformat.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmdist</b> - compute distances between clusterings</td>
- <td><a href="clmdist.html">html</a></td>
- <td><a href="clmdist.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clminfo</b> - performance measures for clusterings</td>
- <td><a href="clminfo.html">html</a></td>
- <td><a href="clminfo.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmmeet</b> - compute intersection of clusterings</td>
- <td><a href="clmmeet.html">html</a></td>
- <td><a href="clmmeet.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmmate</b> - compute best matches between two clusterings</td>
- <td><a href="clmmate.html">html</a></td>
- <td><a href="clmmate.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmimac</b> - Interpret Matrices (c.q. MCL iterands) As Clusterings</td>
- <td><a href="clmimac.html">html</a></td>
- <td><a href="clmimac.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmresidue</b> - extend subgraph clusterings onto encompassing graph</td>
- <td><a href="clmresidue.html">html</a></td>
- <td><a href="clmresidue.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmorder</b> - reorder indices to represent blocks from different clusterings</td>
- <td><a href="clmorder.html">html</a></td>
- <td><a href="clmorder.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>clmclose</b> - fetch connected components from graphs or subgraphs</td>
- <td><a href="clmclose.html">html</a></td>
- <td><a href="clmclose.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Dealing with matrices</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
-<tr>
- <td><b>mcxio</b> - the mcl matrix format specification</td>
- <td><a href="mcxio.html">html</a></td>
- <td><a href="mcxio.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcx</b> - interface to basic matrix operations</td>
- <td><a href="mcx.html">html</a></td>
- <td><a href="mcx.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxsubs</b> - extract submatrices by specifiying sets of nodes and clusters</td>
- <td><a href="mcxsubs.html">html</a></td>
- <td><a href="mcxsubs.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxmap</b> - remap matrix indices / relabel graph nodes</td>
- <td><a href="mcxmap.html">html</a></td>
- <td><a href="mcxmap.ps">ps</a></td>
- </tr>
-<tr>
- <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
- <td><a href="mcxassemble.html">html</a></td>
- <td><a href="mcxassemble.ps">ps</a></td>
- </tr>
-</table>
-
-
-
- <h3 style="margin-top:2em">Application specific parsers and wrappers</h3>
- <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
-
- <tr>
- <th colspan="3">
- <b>BLAST package</b> - Documentation only available if installed with <b>--enable-blast</b>
- </th>
- </tr>
-
- <tr>
- <td><b>mclblastline</b> - pipeline for clustering from blast files</td>
- <td><a href="mclblastline.html">html</a></td>
- <td><a href="mclblastline.ps">ps</a></td>
- </tr>
- <tr>
- <td><b>mcxdeblast</b> - prepare input from blast files</td>
- <td><a href="mcxdeblast.html">html</a></td>
- <td><a href="mcxdeblast.ps">ps</a></td>
- </tr>
-</table>
-
-
-</body>
-</html>
-
-
-
-
diff --git a/doc/mcl.1 b/doc/mcl.1
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-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcl" 1 "16 May 2014" "mcl 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcl \- The Markov Cluster Algorithm, aka the MCL algorithm\&.
-
-This program implements \fBmcl\fP, a cluster algorithm for graphs\&. A single
-parameter controls the granularity of the output clustering, namely the
-\fB-I\fP\ \&\fIinflation\fP option described further below\&.
-In standard usage of the program this parameter is the only one that may
-require changing\&. By default it is set to\ \&2\&.0 and this is a good way to
-start\&. If you want to explore cluster structure in graphs with MCL, vary
-this parameter to obtain clusterings at different levels of granularity\&. A
-good set of starting values is 1\&.4, 2, 4, and 6\&.
-
-The program has a rather large set of options\&. Except for \fB-I\fP
-none affects the clustering method itself\&. The other options are for a
-variety of aspects, such as study of the underlying MCL process (i\&.e\&.
-dumping of iterands), network preprocessing (incorporated for efficiency),
-resource allocation options (for large-scale analyses), output naming
-and placement, output formatting, setting of verbosity levels, and so on\&.
-
-Network construction and reduction techniques should not be considered as
-part of a clustering algorithm\&. Nevertheless particular techniques may
-benefit particular methods or applications\&. In mcl many transformations are
-accessible through the \fB-tf\fP option\&. It can be used for edge
-weight transformations and selection, as well as transformations that act on
-a graph as a whole\&.
-It is for example possible to remove edges with weight below 0\&.7 by issuing
-\fB-tf\fP\ \&\fB\&'gq(0\&.7)\&'\fP, where the quotes are necessary to prevent the shell
-from interpreting the parentheses\&. The option accepts more complicated
-sequences, such as \fB-tf\fP\ \&\fB\&'gq(0\&.7),add(-0\&.7)\&'\fP\&. This causes all
-remaining edge weights to be shifted to the range [0-0\&.3], assuming that the
-input contains correlations\&. Many more transformations are supported, as
-documented in \fBmcxio(5)\fP\&. Examples of graph-wide transformations are
-\fC\&'#knn(<num>)\&'\fP and \fC\&'#ceilnb(<num>)\&'\fP\&. The first only keeps those edges
-that occur in the list of top-\fC<num>\fP edges of highest weight in both of
-its incident nodes\&. The second removes edges from nodes of highest degree
-first, proceeding until all node degrees satisfy the given threshold\&.
-The \fB-pi\fP (pre-inflation) option can be used to increase the
-contrast in edge weights\&. This may be useful when clusterings are coarse and
-fine-grained clusterings are difficult to obtain\&.
-.SH GETTING STARTED
-There are two main modes of invocation\&. The most accessible is
-\fIlabel mode\fP
-which assumes a format alternatively called label input or ABC-format\&.
-The input is then a file or stream in which each
-line encodes an edge in terms of two labels (the \&'A\&' and the \&'B\&')
-and a numerical value (the \&'C\&'), all separated
-by white space\&. The most basic example of usage is this:
-
-.di ZV
-.in 0
-.nf \fC
- \fBmcl\fP <-|fname> \fB--abc\fP \fB-o\fP\ \&\fIfname-out\fP
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The output is then a file where each line is a cluster of tab-separated
-labels\&.
-If clustering is part of a larger workflow where it
-is desirable to analyse and compare multiple clusterings,
-then it is a good idea to use native mode rather than ABC\ \&mode\&.
-The reason for this is that native mode is understood
-by all programs in the mcl suite\&. It is a more stringent
-and unambiguous format, and hence more suitable for data exchange\&.
-The reader is refered to \fBclmprotocols(5)\fP for more information\&.
-.SH SYNOPSIS
-The example invocation below assumes matrix input, as explained above
-and described in the \fBmcxio(5)\fP section\&. Switching to label mode requires
-the input file to be in ABC-format and the addition of the \fB--abc\fP
-option\&.
-
-\fBmcl\fP <-|fname>
-\fB[-I\fP <num> (\fIinflation\fP)\fB]\fP
-\fB[-o\fP <str> (\fIfname\fP)\fB]\fP
-
-These options are sufficient in 95 percent of the cases or more\&. The first
-argument must be the name of a file containing a graph/matrix in the mcl
-input format, or a hyphen to read from STDIN\&. With respect to clustering,
-the \fB-I\fP option is foremost relevant\&.
-
-The full listing of \fBmcl\fP options is shown further below, separated
-into parts corresponding with functional aspects such
-as clustering, threading, verbosity, network preprocessing, pruning and resource management,
-automatic output naming, and dumping\&.
-
-\fBBaseline clustering options\fP
-.br
-\fB[-I\fP <num> (\fIinflation\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIfname\fP)\fB]\fP
-
-\fBOutput options\fP
-.br
-\fB[-odir\fP <dname> (\fIdirectory\fP)\fB]\fP
-\fB[--d\fP (\fIuse input directory for output\fP)\fB]\fP
-
-\fBInput options\fP
-.br
-\fB[--abc\fP (\fIexpect/write labels\fP)\fB]\fP
-\fB[--sif\fP (\fIexpect/write labels\fP)\fB]\fP
-\fB[--etc\fP (\fIexpect/write labels\fP)\fB]\fP
-\fB[--expect-values\fP (\fIsif or etc stream contains values\fP)\fB]\fP
-\fB[-use-tab\fP <fname> (\fIuse mapping to write\fP)\fB]\fP
-
-\fBTransform options\fP
-.br
-\fB[-tf\fP <tf-spec> (\fItransform input matrix values\fP)\fB]\fP
-\fB[-abc-tf\fP <tf-spec> (\fItransform input stream values\fP)\fB]\fP
-\fB[--abc-neg-log10\fP (\fItake log10 of stream values, negate sign\fP)\fB]\fP
-\fB[--abc-neg-log\fP (\fItake log of stream values, negate sign\fP)\fB]\fP
-\fB[-icl\fP <fname> (\fIcreate subgraph on clustering\fP)\fB]\fP
-
-\fBCache options\fP
-.br
-\fB[-write-graph\fP <fname> (\fIwrite graph\fP)\fB]\fP
-\fB[-write-graphx\fP <fname> (\fIwrite transformed graph\fP)\fB]\fP
-\fB[-write-expanded\fP <fname> (\fIwrite expanded graph\fP)\fB]\fP
-\fB[--write-limit\fP (\fIwrite mcl process limit\fP)\fB]\fP
-
-\fBInput manipulation options\fP
-.br
-\fB[-pi\fP <num> (\fIpre-inflation\fP)\fB]\fP
-\fB[-ph\fP <num> (\fIpre-inflation, max-bound\fP)\fB]\fP
-\fB[-if\fP <num> (\fIstart-inflation\fP)\fB]\fP
-\fB[--discard-loops=\fP<y/n> (\fIdiscard y/n loops in input\fP)\fB]\fP
-\fB[--sum-loops\fP (\fIset loops to sum of other arcs weights\fP)\fB]\fP
-\fB[-c\fP <num> (\fIreweight loops\fP)\fB]\fP
-
-\fBClustering processing options\fP
-.br
-\fB[-sort\fP <str> (\fIsort mode\fP)\fB]\fP
-\fB[-overlap\fP <str> (\fIoverlap mode\fP)\fB]\fP
-\fB[--force-connected=\fP<y/n> (\fIanalyze components\fP)\fB]\fP
-\fB[--check-connected=\fP<y/n> (\fIanalyze components\fP)\fB]\fP
-\fB[--analyze=\fP<y/n> (\fIperformance criteria\fP)\fB]\fP
-\fB[--show-log=\fP<y/n> (\fIshow log\fP)\fB]\fP
-
-\fBVerbosity options\fP
-.br
-\fB[-q\fP <spec> (\fIlog levels\fP)\fB]\fP
-\fB[-v\fP <str> (\fIverbosity type on\fP)\fB]\fP
-\fB[-V\fP <str> (\fIverbosity type off\fP)\fB]\fP
-\fB[--show\fP (\fIprint (small) matrices to screen\fP)\fB]\fP
-
-\fBThread options\fP
-.br
-\fB[-te\fP <int> (\fI#expansion threads\fP)\fB]\fP
-
-\fBOutput file name and annotation options\fP
-.br
-\fB[-o\fP <str> (\fIfname\fP)\fB]\fP
-\fB[-ap\fP <str> (\fIuse str as file name prefix\fP)\fB]\fP
-\fB[-aa\fP <str> (\fIappend str to suffix\fP)\fB]\fP
-\fB[-az\fP (\fIshow output file name and exit\fP)\fB]\fP
-\fB[-ax\fP (\fIshow output suffix and exit\fP)\fB]\fP
-\fB[-annot\fP <str> (\fIdummy annotation option\fP)\fB]\fP
-
-\fBDump options\fP
-.br
-\fB[-dump-interval\fP <i:j> (\fIdump interval\fP)\fB]\fP
-\fB[-dump-modulo\fP <int> (\fIdump modulo\fP)\fB]\fP
-\fB[-dump-stem\fP <stem> (\fIdump file stem\fP)\fB]\fP
-\fB[-dump\fP <str> (\fItype\fP)\fB]\fP
-\fB[-digits\fP <int> (\fIprinting precision\fP)\fB]\fP
-\fB[--write-binary\fP (\fIwrite matrices in binary format\fP)\fB]\fP
-
-\fBInfo options\fP
-.br
-\fB[--jury-charter\fP (\fIexplains jury\fP)\fB]\fP
-\fB[--version\fP (\fIshow version\fP)\fB]\fP
-\fB[-how-much-ram\fP k (\fIRAM upper bound\fP)\fB]\fP
-\fB[-h\fP (\fImost important options\fP)\fB]\fP
-\fB[--help\fP (\fIone-line description for all options\fP)\fB]\fP
-\fB[-z\fP (\fIshow current settings\fP)\fB]\fP
-\fB[-az\fP (\fIshow output file name and exit\fP)\fB]\fP
-\fB[-ax\fP (\fIshow output suffix and exit\fP)\fB]\fP
-\fB[--show-schemes\fP (\fIshow resource schemes\fP)\fB]\fP
-
-\fBImplementation options\fP
-.br
-\fB[-sparse\fP <int> (\fIsparse matrix multiplication threshold\fP)\fB]\fP
-
-\fBPruning options\fP
-.br
-The following options all pertain to the various pruning strategies that can
-be employed by \fBmcl\fP\&. They are described in the \fBPRUNING OPTIONS\fP
-section, accompanied by a description of the mcl pruning strategy\&.
-If your graphs are huge
-and you have an appetite for tuning, have a look at the following:
-
-\fB[-scheme\fP <int> (\fIresource scheme\fP)\fB]\fP
-\fB[-resource\fP <int> (\fIper-node resource maximum\fP)\fB]\fP
-\fB[-p\fP <num> (\fIcutoff\fP)\fB]\fP
-\fB[-P\fP <int> (\fI1/cutoff\fP)\fB]\fP
-\fB[-S\fP <int> (\fIselection number\fP)\fB]\fP
-\fB[-R\fP <int> (\fIrecovery number\fP)\fB]\fP
-\fB[-pct\fP <int> (\fIrecover percentage\fP)\fB]\fP
-\fB[-warn-pct\fP <int> (\fIprune warn percentage\fP)\fB]\fP
-\fB[-warn-factor\fP <int> (\fIprune warn factor\fP)\fB]\fP
-
-The first argument of \fBmcl\fP must be a file name, but some options are allowed
-to appear as the first argument instead\&. These are the options that cause
-mcl to print out information of some kind, after which it will gracefully
-exit\&. The full list of these options is
-
-\fB-z\fP,
-\fB-h\fP,
-\fB--help\fP,
-\fB--version\fP,
-\fB--show-settings\fP,
-\fB--show-schemes\fP,
-\fB--jury-charter\fP\&.
-.SH DESCRIPTION
-
-\fBmcl\fP implements the \fBMCL algorithm\fP, short for the \fBMarkov cluster
-algorithm\fP, a cluster algorithm for graphs developed by Stijn van Dongen at
-the Centre for Mathematics and Computer Science in Amsterdam, the
-Netherlands\&. The algorithm simulates flow using two simple algebraic
-operations on matrices\&.
-The inception of this flow process and the theory behind it are
-described elsewhere (see \fBREFERENCES\fP)\&. Frequently asked questions
-are answered in the \fBmclfaq(7)\fP section\&.
-The program described here is a fast threaded implementation written by the
-algorithm\&'s creator with contributions by several others\&. Anton Enright
-co-implemented threading; see the \fBHISTORY/CREDITS\fP section for a complete
-account\&.
-See the \fBAPPLICABILITY\fP section for a description of the type of
-graph mcl likes best, and for a qualitative assessment of its speed\&.
-\fBmcl\fP is accompanied by several other utilities for analyzing clusterings and
-performing matrix and graph operations; see the \fBSEE ALSO\fP section\&.
-
-The first argument is the input file name,
-or a single hyphen to read from stdin\&. The rationale for
-making the name of the input file a fixed parameter is that you typically do
-several runs with different parameters\&. In command line mode it is
-pleasant if you do not have to skip over an immutable parameter all the
-time\&.
-
-The \fB-I\fP\ \&\fIf\fP option is the main control,
-affecting cluster granularity\&.
-In finding good \fBmcl\fP parameter settings for a particular domain,
-or in finding cluster structure at different levels of granularity,
-one typically runs mcl multiple times for varying values of f (refer
-to the \fB-I\fP\ \&\fIinflation\fP option for further information)\&.
-
-\fBNOTE\fP MCL interprets the matrix
-entries or graph edge weights as \fBsimilarities\fP, and it likes
-\fBundirected input graphs\fP best\&. It can handle directed graphs, but any
-node pair (i,j) for which w(i,j) is much smaller than w(j,i) or vice versa
-will presumably have a slightly negative effect on the clusterings output by
-mcl\&. Many such node pairs will have a distinctly negative effect, so try to
-make your input graphs undirected\&. How your edge weights are computed may
-affect mcl\&'s performance\&. In protein clustering, one way to go is to
-choose the negated logarithm of the BLAST probabilities (see
-\fBREFERENCES\fP)\&.
-
-\fBmcl\fP\&'s default parameters should make it quite fast under almost all
-circumstances\&. Taking default parameters, mcl has been used to generate
-good protein clusters on 133k proteins, taking 10 minutes running time on a
-Compaq ES40 system with four alpha EV6\&.7 processors\&. It has been applied
-(with good results) to graphs with two million nodes, and if you have the memory
-(and preferably CPUs as well) nothing should stop you from going further\&.
-
-For large graphs, there are several groups of parameters available for
-tuning the mcl computing process, should it be necessary\&. The easiest thing
-to do is just vary the \fB-scheme\fP option\&. This
-triggers different settings for the group of pruning parameters
-\fB-p/-P\fP, \fB-R\fP, \fB-S\fP, and
-\fB-pct\fP\&. The default setting corresponds with
-\fB-scheme\fP\ \&\fB6\fP\&.
-When doing multiple mcl runs for the same graphs with different
-\fB-I\fP settings (for obtaining clusterings at different levels
-of granularity), it can be useful to factor out the first bit
-of computation that is common to all runs, by using
-the \fB-write-expanded\fP option one time
-and then using \fB-if\fP\ \&\fIinflation\fP for each run in the set\&.
-Whether mcl considers a graph large depends mainly on the graph
-connectivity; a highly connected graph on 50,000 nodes is large to
-mcl (so that you might want to tune resources) whereas a sparsely
-connected graph on 500,000 nodes may be business as usual\&.
-
-\fBmcl\fP is a memory munger\&. Its precise appetite depends on the resource
-settings\&. You can get a rough (and usually much too pessimistic) upper
-bound for the amount of RAM that is needed by using the
-\fB-how-much-ram\fP option\&. The corresponding
-entry in this manual page contains the simple formula via which the upper
-bound is computed\&.
-
-Other options of interest are the option to specify threads
-\fB-te\fP, and the verbosity-related options
-\fB-v\fP and \fB-V\fP\&.
-The actual settings are shown with \fB-z\fP, and for graphs with
-at most 12 nodes or so you can view the MCL matrix iterands on screen
-by supplying \fB--show\fP (this may give some
-more feeling)\&.
-
-MCL iterands allow a generic interpretation as clusterings as well\&. The
-clusterings associated with early iterands may contain a fair amount of
-overlap\&. Refer to the \fB-dump\fP option, the \fBmclfaq(7)\fP
-manual, and the \fBclm imac\fP utility (Interpret Matrices As Clusterings)\&.
-Use \fBclm imac\fP only if you have a special reason; the normal usage of \fBmcl\fP is
-to do multiple runs for varying \fB-I\fP parameters and use the
-clusterings output by mcl itself\&.
-
-Under very rare circumstances, \fBmcl\fP might get stuck in a seemingly infinite
-loop\&. If the number of iterations exceeds a hundred and the \fIchaos\fP
-indicator remains nearly constant (presumably around value 0\&.37), you can
-force mcl to stop by sending it the ALRM signal (usually done
-by \fBkill -s ALRM\fP \fIpid\fP)\&. It will finish the current
-iteration, and interpret the last iterand as a clustering\&. Alternatively, you
-can wait and mcl might converge by itself or it will certainly stop after
-10,000 iterations\&. The
-most probable explanation for such an infinite loop is that the input graph
-contains the flip-flop graph of node size three as a subgraph\&.
-
-The creator of this page feels that manual pages are a valuable resource,
-that online html documentation is also a good thing to have, and
-that info pages are way \fIway\fP ahead of their time\&. The
-\fBNOTES\fP section explains how this page was created\&.
-
-In the \fBOPTIONS\fP section options are listed in order of
-importance, with related options grouped together\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-I\fP <num> (\fIinflation\fP)"
-\&
-.br
-Sets the main inflation value to \fI<num>\fP\&. This value is the main handle
-for affecting cluster granularity\&. It is usually chosen somewhere
-in the range [1\&.2-5\&.0]\&. \fB-I\fP\ \&\fB5\&.0\fP will tend to result
-in fine-grained clusterings, and \fB-I\fP\ \&\fB1\&.2\fP will tend to
-result in very coarse grained clusterings\&. Your mileage will vary
-depending on the characteristics of your data\&. That is why it is
-a good idea to test the quality and coherency of your clusterings
-using \fBclm dist\fP and \fBclm info\fP\&. This will most likely reveal that
-certain values of \fB-I\fP are simply not right for your data\&. The
-\fBclm dist\fP section contains a discussion of how to use the cluster
-validation tools shipped with \fBmcl\fP (see the \fBSEE ALSO\fP section)\&.
-
-With low values for \fB-I\fP, like \fB-I\fP\ \&\fB1\&.2\fP, you should be
-prepared to use more resources in order to maintain quality of
-clusterings, i\&.e\&. increase the argument to the
-\fB-scheme\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-odir\fP <dname> (\fIoutput directory name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--d\fP (\fIuse input directory for output\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The default mode of output creation for \fBmcl\fP is to create a file name that
-uses the input file name stripped of any leading path components, augmented
-with a prefix \&'\fCout\&.\fP\&' and a suffix encoding pivotal \fBmcl\fP parameters\&.
-This will usually be the inflation value which is the argument to the \fB-I\fP
-option\&. By default the output file is written in the current directory\&.
-For example, if the input is named \fCdata/small\&.mci\fP for example and
-inflation is set to three, the output file will be named
-\fCout\&.small\&.mci\&.I30\fP\&.
-
-This behaviour can be overridden in various ways\&. The \fB-o\fP option simply
-specifies the output file name, which may include path components that
-should exist\&. It is possible to send the clustering to STDOUT by supplying
-\fB-o\fP\ \&\fB-\fP\&. With the \fB-odir\fP\ \&\fI<dname>\fP option \fBmcl\fP constructs the
-output file name as before, but writes the file in the directory \fI<dname>\fP\&.
-Finally, the option \fB--d\fP is similar but more specific in that \fBmcl\fP
-will write the output in the directory specified by the path component of
-the input file, that is, the directory in which the input file resides\&.
-
-If either one of
-\fB--abc\fP, \fB--sif\fP, \fB--etc\fP or
-\fB-use-tab\fP\ \&\fItab-file\fP is used the output will be in label format\&.
-Otherwise the clustering is output in the mcl matrix format; see the \fBmcxio(5)\fP
-section for more information on this\&. Refer also to the group of options
-discussed at \fB--abc\fP\&.
-
-Look at the \fB-ap\fP\ \&\fIprefix\fP option and its siblings for the
-automatic naming constructions employed by \fBmcl\fP if the \fB-o\fP option is
-not used\&.
-.in -2m
-
-.ZI 2m "\fB-c\fP <num> (\fIreweight loops\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--sum-loops\fP (\fIset loops to sum of other arcs weights\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-With the \fB-c\fP\ \&\fI<num>\fP option, as the final step of loop computation
-(i\&.e\&. after initialization and shadowing) all loop weights are multiplied by
-\fB<num>\fP, if supplied\&.
-.in -2m
-
-.ZI 2m "\fB--discard-loops\fP=<y/n> (\fIdiscard loops in input\fP)"
-\&
-.br
-By default \fBmcl\fP will remove any loops that are present in the input\&. Use
-\fB--discard-loops\fP=\fBn\fP to turn this off\&. Bear in mind that loops will
-still be modified in all cases where the loop weight is not maximal among
-the list of edge weights for a given node\&.
-.in -2m
-
-.ZI 2m "\fB--abc\fP (\fIexpect/write labels\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--sif\fP (\fIexpect/write labels\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--etc\fP (\fIexpect/write labels\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--expect-values\fP (\fIexpect label:weight format\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-use-tab\fP <fname> (\fIuse mapping to write\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These items all relate to label input and/or label output\&.
-\fB--abc\fP tells \fBmcl\fP to expect label input and output clusters
-in terms of those labels\&. This simple format expects two or
-three fields separated by white space on each line\&.
-The first and second fields are interpreted as labels specifying
-source and destination node respectively\&. The third field, if present,
-specifies the weight of the arc connecting the two nodes\&.
-
-The option \fB--sif\fP tells \fBmcl\fP to expect SIF (Simple Interaction File)
-format\&. This format is line based\&. The first two fields
-specify the source node (as a label) and the relationship type\&. An arbitrary number
-of fields may follow, each containing a label identifying a destination node\&.
-The second field is simply ignored by \fBmcl\fP\&.
-As an extension to the SIF format
-weights may optionally follow the labels, separated from them with a colon character\&.
-It is in this case necessary to use the \fB--expect-values\fP option\&.
-The \fB--etc\fP option expects a format identical in all respects except
-that the relationship type is not present, so that all fields after the first
-are interpreted as destination labels\&.
-
-\fB-use-tab\fP is only useful when matrix input is used\&.
-It will use the tab file to convert the output to labels; it does
-not fail on indices missing from the tab file, but will bind
-these to generated dummy labels\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-abc-tf\fP <tf-spec> (\fItransform input stream values\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--abc-neg-log10\fP (\fItake log10 of stream values, negate sign\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--abc-neg-log\fP (\fItake log of stream values, negate sign\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-\fB-tf\fP transforms the values of the input matrix according
-to \fB<tf-spec>\fP\&. \fB-abc-tf\fP transforms the stream values
-(when \fB--abc\fP is used) according to \fB<tf-spec>\fP\&.
-\fB--abc-neg-log\fP and \fB--abc-neg-log10\fP
-imply that the stream input values are
-replaced by the negation of their log or log10 values, respectively\&.
-The reason for their existence is documented in \fBmcxio(5)\fP\&.
-For a description of the transform language excpected/accepted
-in \fB<tf-spec>\fP refer to the same\&.
-.in -2m
-
-.ZI 2m "\fB-icl\fP <fname> (\fIcreate subgraph on clustering\fP)"
-\&
-.br
-
-With this option \fBmcl\fP will subcluster the provided clustering\&.
-It does so by removing, first of all, all edges from the input
-graph that connect different clusters\&.
-The resulting graph consists of different
-components, at least as many as there are clusters in
-the input clustering\&. This graph is then subjected to transformations,
-if any are specified, and then clustered\&.
-The output name is constructed by appending the normal mcl-created
-file name suffix to the name of the input clustering\&.
-.in -2m
-
-.ZI 2m "\fB-write-graph\fP <fname> (\fIwrite graph\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-write-graphx\fP <fname> (\fIwrite transformed graph\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-write-expanded\fP <fname> (\fIwrite expanded graph\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-limit\fP (\fIwrite mcl process limit\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The first two options are somewhat outdated, in that the prefered way of
-loading networks is by using \fBmcxload(1)\fP\&. The option
-\fB-write-expanded\fP can be useful for exploring more complicated input
-transformations that incorporate an expansion step, but is not really
-relevant for production use\&. The last option is mainly educational and for
-analyzing the \fBmcl\fP process itself\&.
-.in -2m
-
-.ZI 2m "\fB-scheme\fP <num> (\fIuse a preset resource scheme\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-resource\fP <num> (\fIallow n neighbours throughout\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-There are currently seven different resource schemes, indexed 1\&.\&.7\&.
-High schemes result in more expensive computations that may possibly be
-more accurate\&. The default scheme is 4\&. When \fBmcl\fP is done, it will give a
-grade (the so called \fIjury synopsis\fP) to the appropriateness of the
-scheme used\&. \fIA low grade does not necessarily imply that the
-resulting clustering is bad\fP - but anyway, a low grade should be reason
-to try for a higher scheme\&.
-
-Use the \fB-resource\fP\ \&\fI<num>\fP option to cap for each nodes the number of
-neighbours tracked during computation at \fI<num>\fP nodes\&.
-
-The \fBPRUNING OPTIONS\fP section contains an elaborate description
-of the way \fBmcl\fP manages resources, should you be interested\&.
-In case you are worried about the validation of the resulting
-clusterings, the \fBmclfaq(7)\fP section
-has several entries discussing this issue\&. The bottom line is
-that you have to compare the clusterings resulting from different
-schemes (and otherwise identical parameters) using utilities
-such as \fBclm dist\fP, \fBclm info\fP on the one hand, and your
-own sound judgment on the other hand\&.
-
-If your input graph is extremely dense, with an average node degree
-(i\&.e\&. the number of neighbours per node) that is somewhere above
-500, you may need to filter the input graph by removing edges,
-for example by using one of \fB-tf\fP\ \&\fB\&'#ceilnb()\&'\fP
-or \fB-tf\fP\ \&\fB\&'#knn()\&'\fP\&.
-.in -2m
-
-.ZI 2m "\fB--show-schemes\fP (\fIshow preset resource schemes\fP)"
-\&
-.br
-Shows the explicit settings to which the different preset schemes
-correspond\&.
-
-The characteristics are written in the same format (more or less) as
-the output triggered by \fB-v\fP\ \&\fBpruning\fP\&.
-.in -2m
-
-.ZI 2m "\fB-V\fP <str> (\fIverbosity type off\fP)"
-\&
-.br
-See the \fB-v\fP option below\&.
-.in -2m
-
-.ZI 2m "\fB-v\fP <str> (\fIverbosity type on\fP)"
-\&
-.br
-These are the different verbosity modes:
-
-\fBpruning\fP
-.br
-\fBexplain\fP
-.br
-\fBcls\fP
-.br
-\fBall\fP
-.in -2m
-
-.ZI 2m "\fB-q\fP <spec> (\fIlog levels\fP)"
-\&
-.br
-
-To make mcl as quiet as can be, add
-\fB-q\fP\ \&\fBx\fP \fB-V\fP\ \&\fBall\fP to the command line\&.
-
-The \fB-q\fP option governs a general logging mechanism\&.
-The format accepted is described in the \fBtingea\&.log(7)\fP manual page\&.
-
-The other options govern verbosity levels specific to mcl\&. \fB-v\fP\ \&\fBall\fP
-turns them all on, \fB-V\fP\ \&\fBall\fP turns them all off\&. \fB-v\fP\ \&\fIstr\fP and
-\fB-V\fP\ \&\fIstr\fP turn on/off the single mode \fIstr\fP (for \fIstr\fP
-equal to one of \fBpruning\fP, \fBcls\fP, or \fBexplain\fP)\&. Each verbosity
-mode is given its own entry below\&.
-.in -2m
-
-.ZI 2m "\fB-v\fP\ \&\fBexplain\fP"
-\&
-.br
-This mode causes the output of explanatory headers illuminating the
-output generated with the \fBpruning\fP verbosity mode\&.
-.in -2m
-
-.ZI 2m "\fB-v\fP\ \&\fBpruning\fP"
-\&
-.br
-This mode causes output of resource-related quantities\&. It has
-a separate entry in the PRUNING OPTIONS section\&.
-.in -2m
-
-.ZI 2m "\fB-v\fP\ \&\fBcls\fP"
-\&
-.br
-This mode (on by default) prints a terse list of characteristics of the
-clusterings associated with intermediate iterands\&. The characteristics are
-\fBE/V\fP, \fBcls\fP, \fBolap\fP, and \fBdd\fP\&. They respectively stand for the
-number of outgoing arcs per node (as an average), the number of clusters in
-the overlapping clustering associated with the iterand, the number of nodes
-in overlap, and the \fIdag depth\fP associated with the DAG (directed acyclic
-graph) associated with the iterand\&. For more information on this DAG refer
-to the \fB-dump\fP option description in this manual and also
-\fBmclfaq(7)\fP\&.
-
-\fBStandard log information\fP
-.br
-
-.ZI 5m "m-ie"
-This gives the ratio of (1) the number of edges after initial expansion, before pruning, to
-(2) the number of edges of the current iterand\&.
-.in -5m
-.ZI 5m "m-ex"
-This gives the ratio of (1) the number of edges after expansion (including pruning), to
-(2) the number of edges of the current iterand\&.
-.in -5m
-.ZI 5m "i-ex"
-This gives the ratio of (1) the number of edges after expansion (including pruning), to
-(2) the number of edges of the original input graph\&.
-.in -5m
-.ZI 5m "fmv"
-This gives the percentage of nodes (matrix columns) for which full matrix/vector
-computation was used (as opposed to using a sparse technique)\&.
-.in -5m
-.in -2m
-
-.ZI 2m "\fB-aa\fP <str> (\fIappend <str> to suffix\fP)"
-\&
-.br
-See the \fB-ap\fP option below\&.
-.in -2m
-
-.ZI 2m "\fB-ap\fP <str> (\fIuse <str> as file name prefix\fP)"
-\&
-.br
-If the \fB-o\fP\ \&\fIfname\fP option is not used,
-\fBmcl\fP will create a file name (for writing output to) that
-should uniquely characterize the important parameters used in the
-current invocation of mcl\&. The default format is \fBout\&.fname\&.suf\fP,
-where \fBout\fP is simply the literal string \fCout\fP, \fBfname\fP is the
-first argument containing the name of the file (with the graph) to be
-clustered, and where \fBsuf\fP is the suffix encoding a set of parameters
-(described further below)\&.
-
-The \fB-ap\fP\ \&\fIstr\fP option specifies a prefix to use
-rather than \fBout\&.fname\fP as sketched above\&.
-However, \fBmcl\fP will interpret the character \&'=\&', if present
-in \fIstr\fP, as a placeholder for the input file name\&.
-
-If the \fB-aa\fP\ \&\fIstr\fP option is used, \fBmcl\fP will append
-\fBstr\fP to the suffix \fBsuf\fP created by itself\&.
-You can use this if you need to encode some extra information in the
-file name suffix\&.
-
-The suffix is constructed as follows\&. The \fB-I\fP\ \&\fIf\fP
-and \fB-scheme\fP parameter are always encoded\&.
-Other options, such as \fB-pi\fP\ \&\fIf\fP and \fB-knn\fP
-are only encoded if they are used\&. Any real argument \fIf\fP
-is encoded using \fIexactly one\fP trailing digit behind the decimal
-separator (which itself is not written)\&. The setting \fB-I\fP\ \&\fB3\&.14\fP
-is thus encoded as I31\&. The \fB-scheme\fP option is encoded using the
-letter \&'s\&', all other options mentioned here are encoded as themselves
-(stripped of the hyphen)\&. For example
-
-.di ZV
-.in 0
-.nf \fC
-mcl small\&.mci -I 3 -c 2\&.5 -pi 0\&.8 -scheme 5
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-results in the file name \fCout\&.small\&.mci\&.I30s5c25pi08\fP\&.
-If you want to know beforehand what file name will be produced,
-use the \fB-az\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-az\fP (\fIshow output file name and exit\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ax\fP (\fIshow output suffix and exit\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-If \fBmcl\fP automatically constructs a file name, it can be helpful to known
-beforehand what that file name will be\&. Use \fB-az\fP and mcl will
-write the file name to STDOUT and exit\&. This can be used if mcl is
-integrated into other software for which the automatic creation of
-unique file names is convenient\&.
-
-By default mcl incorporates the input file name into the output file
-name and appends a short suffix describing the most important
-option settings\&. Use \fB-ax\fP to find out what that suffix is\&.
-This can be useful in wrapper pipeline scripts such as clxcoarse\&.
-.in -2m
-
-.ZI 2m "\fB-annot\fP <str> (\fIdummy annotation option\fP)"
-\&
-.br
-\fBmcl\fP writes the command line with which it was invoked to the output
-clustering file\&. Use this option to include any additional
-information\&. MCL does nothing with this option except copying
-it as just described\&.
-.in -2m
-
-.ZI 2m "\fB-te\fP <int> (\fI#expansion threads\fP)"
-\&
-.br
-Threading is useful if you have a multi-processor system\&. \fBmcl\fP will
-spawn \fIk\fP threads of computation\&. If these are computed
-in parallel (this depends on the number of CPUs available to the
-mcl process) it will speed up the process accordingly\&.
-
-When threading, it is best not to turn on pruning verbosity
-mode if you are letting mcl run unattended, unless you want to
-scrutinize its output later\&. This is because it makes \fBmcl\fP run
-somewhat slower, although the difference is not dramatic\&.
-.in -2m
-
-.ZI 2m "\fB-pi\fP <num> (\fIpre-inflation\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ph\fP <num> (\fIpre-inflation, max-bound\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-If used, \fBmcl\fP will apply inflation one time to the input graph
-before entering the main process\&. This can be useful for
-making the edge weights in a graph either more homogeneous (which
-may result in less granular clusterings) or more heterogeneous
-(which may result in more granular clusterings)\&.
-Homogeneity is achieved for values \fI<num>\fP less than one,
-heterogeneity for values larger than one\&.
-Values to try are normally in the range \fC[2\&.0,10\&.0]\fP\&.
-
-The \fB-ph\fP option is special in that it does not rescale
-columns to be stochastic\&. Instead, it rescales columns so that
-the maximum value found in the column stays the same after
-inflation was applied\&. There is little significance to this,
-and what little there is is undocumented\&.
-.in -2m
-
-.ZI 2m "\fB-if\fP <num> (\fIstart-inflation\fP)"
-\&
-.br
-If used, \fBmcl\fP will apply inflation one time to the input graph
-before entering the main process\&. The difference with
-\fB-pi\fP is that with the latter option mcl may apply
-certain transformations after reading in the matrix such
-as adding or modifying loops\&. The purpose of
-the \fB-if\fP (mnemonic for \fIinflation-first\fP)
-option is to use it on graphs saved
-with the \fB--write-expanded\fP option and convey
-to mcl that it should not apply those transformations\&.
-.in -2m
-
-.ZI 2m "\fB-dump-interval\fP <i:j> (\fIdump interval\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-dump-interval\fP\ \&\fIall\fP"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Dump during iterations i\&.\&.j-1\&. Use \fIall\fP to dump in all
-iterations\&. See the \fB-dump\fP\ \&\fIstr\fP option below\&.
-.in -2m
-
-.ZI 2m "\fB-dump-modulo\fP <int> (\fIdump i+0\&.\&.i+<int>\&.\&.\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Sampling rate: select only these iterations in the dump interval\&.
-See the \fB-dump\fP\ \&\fIstr\fP option below\&.
-.in -2m
-
-.ZI 2m "\fB-dump-stem\fP <stem> (\fIfile stem\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Set the the stem for file names of dumped
-objects (default \fImcl\fP)\&. See the \fB-dump\fP\ \&\fIstr\fP option below\&.
-.in -2m
-
-.ZI 2m "\fB-dump\fP <str> (\fItype\fP)"
-\&
-.br
-\fIstr\fP is checked for substring occurrences of the following entries\&.
-Repeated use of \fB-dump\fP is also allowed\&.
-
-\fBite\fP
-.br
-\fBdag\fP
-.br
-\fBcls\fP
-.br
-\fBchr\fP
-.br
-\fBlines\fP
-.br
-\fBcat\fP
-
-\fBlines\fP and \fBcat\fP change the mode of dumping\&. The first
-changes the dump format to a line based pairwise format rather
-than the default mcl matrix format\&. The second causes all
-dumped items to be dumped to the default stream used for the
-output clustering, which is appended at the end\&.
-
-The \fBite\fP option writes \fBmcl\fP iterands to file\&. The \fBcls\fP
-option writes clusterings associated with mcl iterands to file\&.
-These clusters are obtained from a particular directed acyclic graph
-(abbreviated as DAG) associated with each iterand\&. The \fBdag\fP option
-writes that DAG to file\&. The DAG can optionally be further
-pruned and then again be interpreted as a
-clustering using \fBclm imac\fP, and \fBclm imac\fP can also
-work with the matrices written using the \fBite\fP option\&.
-It should be noted that clusterings associated with intermediate
-iterands may contain overlap, which is interesting in
-many applications\&. For more information
-refer to \fBmclfaq(7)\fP and the \fBREFERENCES\fP section below\&.
-
-The \fBresult\fP option dumps the usual MCL clustering\&.
-
-The \fBchr\fP option says, for each iterand I, to output a matrix C with
-characteristics of I\&. C has the same number of columns as I\&. For each
-column k in C, row entry 0 is the diagonal or \&'loop\&' value of column k in
-I \fIafter\fP expansion and pruning, and \fIbefore\fP inflation and
-rescaling\&. Entry 1 is the loop value \fIafter\fP inflation and rescaling\&.
-Entry 2 is the center of column k (the sum of its entries squared)
-computed \fIafter\fP expansion and \fIbefore\fP pruning, entry 3 is the
-maximum value found in that column at the same time\&. Entry 4 is the
-amount of mass kept for that column \fIafter pruning\fP\&.
-
-The \fB-ds\fP option sets the stem for file names of dumped
-objects (default \fImcl\fP)\&. The \fB-di\fP and \fB-dm\fP
-options allow a selection of iterands to be made\&.
-.in -2m
-
-.ZI 2m "\fB-digits\fP <int> (\fIprinting precision\fP)"
-\&
-.br
-This has two completely different uses\&. It sets
-the number of decimals used for pretty-printing \fBmcl\fP iterands
-when using the \fB--show\fP option (see below),
-and it sets the number of decimals used for writing
-the expanded matrix when using the \fB-write-expanded\fP option\&.
-.in -2m
-
-.ZI 2m "\fB--show\fP (\fIprint matrices to screen\fP)"
-\&
-.br
-Print matrices to screen\&. The number of significant digits to be
-printed can be tuned with \fB-digits\fP\ \&\fIn\fP\&. An 80-column screen
-allows graphs (matrices) of size up to 12(x12) to be printed with
-three digits precision (behind the comma), and of size up to 14(x14)
-with two digits\&. This can give you an idea of how \fBmcl\fP operates,
-and what the effect of pruning is\&.
-Use e\&.g\&. \fB-S\fP\ \&\fB6\fP for such
-a small graph and view the MCL matrix iterands with \fB--show\fP\&.
-.in -2m
-
-.ZI 2m "\fB--write-binary\fP (\fIoutput format\fP)"
-\&
-.br
-Write matrix dump output in binary mcl format rather
-than interchange mcl format (the default)\&. Note that \fBmcxconvert\fP
-can be used to convert each one into the other\&.
-See \fBmcxio(5)\fP and \fBmcx(1)\fP for more information\&.
-.in -2m
-
-.ZI 2m "\fB-sort\fP <str> (\fIsort mode\fP)"
-\&
-.br
-\fIstr\fP can be one of \fBlex\fP, \fBsize\fP, \fBrevsize\fP,
-or \fBnone\fP\&. The default is \&'revsize\&', in which the largest
-clusters come first\&. If the mode is \&'size\&', smallest clusters
-come first, if the mode is \&'lex\&', clusters are ordered
-lexicographically, and if the mode is \&'none\&', the order
-is the same as produced by the procedure used by mcl to
-map matrices onto clusterings\&.
-.in -2m
-
-.ZI 2m "\fB-overlap\fP <str> (\fIoverlap mode\fP)"
-\&
-.br
-Mode \fIkeep\fP causes mcl to retain overlap should this improbable event
-occur\&. In theory, \fBmcl\fP may generate a clustering that contains overlap,
-although this almost never happens in practice, as it requires some
-particular type of symmetry to be present in the input graph (not just any
-symmetry will do)\&. Mathematically speaking, this is a conjecture and not a
-theorem, but the present author wil eat his shoe if it fails to be true (for
-marzipan values of shoe)\&. It is easy though to construct an input graph for
-which certain mcl settings result in overlap - for example a line graph on
-an odd number of nodes\&. The default is to excise overlapping parts and
-introduce them as clusters in their own right\&. It is possible to allocate
-nodes in overlap to the first cluster in which they occur (i\&.e\&. rather
-arbitrarily), corresponding with mode \fIcut\fP\&.
-
-In mode \fIsplit\fP mcl will put all nodes in overlap into
-separate clusters\&. These clusters are chosen such that
-two nodes are put in the same new cluster if and only if
-they always occur paired in the clusters of the
-overlapping clustering\&.
-
-This option has no effect on the clusterings that are
-output when using \fB-dump\fP\ \&\fIcls\fP -
-the default for those is that overlap is not touched,
-and this default can not yet be overridden\&.
-.in -2m
-
-.ZI 2m "\fB--force-connected\fP=<y/n> (\fIanalyze components\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--check-connected\fP=<y/n> (\fIanalyze components\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-If the input graph has strong bipartite characteristics,
-mcl may yield clusters that do not correspond to connected
-components in the input graph\&. Turn one of these modes on to
-analyze the resultant clustering\&.
-
-If loose clusters are found
-they will be split into subclusters corresponding to
-connected components\&.
-With \fB--force-connected\fP=\fIy\fP mcl will write the
-corrected clustering to the normal output file, and the old clustering
-to the same file with suffix \fCorig\fP\&.
-With \fB--check-connected\fP=\fIy\fP mcl will write the
-loose clustering to the normal output file, and the corrected clustering
-to the same file with suffix \fCcoco\fP\&.
-
-These options are not on by default, as the analysis
-is currently (overly) time-consuming
-and mcl\&'s behaviour actually makes some sense
-(when taking bipartite characteristics into account)\&.
-.in -2m
-
-.ZI 2m "\fB--analyze\fP=<y/n> (\fIperformance criteria\fP)"
-\&
-.br
-With this mode turned on, \fBmcl\fP will reread the input matrix
-and compute a few performance criteria and attach them to
-the output file\&. Off by default\&.
-.in -2m
-
-.ZI 2m "\fB--show-log\fP=<y/n> (\fIshow log\fP)"
-\&
-.br
-Shows the log with process characteristics on STDOUT\&.
-By default, this mode is off\&.
-.in -2m
-
-.ZI 2m "\fB--jury-charter\fP (\fIexplains jury\fP)"
-\&
-.br
-Explains how the jury synopsis is computed from the jury marks\&.
-.in -2m
-
-.ZI 2m "\fB--version\fP (\fIshow version\fP)"
-\&
-.br
-Show version\&.
-.in -2m
-
-.ZI 2m "\fB-how-much-ram\fP <int> (\fIRAM upper bound\fP)"
-\&
-.br
-\fB<int>\fP is interpreted as the number of nodes of an input graph\&.
-mcl will print the maximum amount of RAM it needs for its computations\&.
-The formula for this number in bytes is:
-
-.di ZV
-.in 0
-.nf \fC
- 2 * c * k * <int>
-
- 2 : two matrices are concurrently held in memory\&.
- c : mcl cell size (as shown by -z)\&.
- <int>: graph cardinality (number of nodes)\&.
- k : MAX(s, r)\&.
- s : select number (-S, -scheme options)\&.
- r : recover number (-R, -scheme options)\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This estimate will usually be too pessimistic\&. It does assume though that
-the average node degree of the input graph does not exceed k\&. The
-\fB-how-much-ram\fP option takes other command-line arguments into
-account (such as \fB-S\fP and \fB-R\fP), and it expresses the
-amount of RAM in megabyte units\&.
-.in -2m
-
-.ZI 2m "\fB-h\fP (\fIshow help\fP)"
-\&
-.br
-Shows a selection of the most important \fBmcl\fP options\&.
-.in -2m
-
-.ZI 2m "\fB--help\fP (\fIshow help\fP)"
-\&
-.br
-Gives a one-line description for all options\&.
-.in -2m
-
-.ZI 2m "\fB-z\fP (\fIshow settings\fP)"
-\&
-.br
-Show current settings for tunable parameters\&.
-\fB--show-settings\fP is a synonym\&.
-.in -2m
-.SH PRUNING OPTIONS
-
-.ZI 2m "\fB-p\fP <num> (\fIcutoff\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-P\fP <int> (\fI1/cutoff\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-S\fP <int> (\fIselection number\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-R\fP <int> (\fIrecover number\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-pct\fP <pct> (\fIrecover percentage\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-After computing a new (column stochastic) matrix vector during expansion
-(which is matrix multiplication c\&.q\&. squaring), the vector is
-successively exposed to different pruning strategies\&. The intent of
-pruning is that many small entries are removed while retaining much of
-the stochastic mass of the original vector\&. After pruning, vectors are
-rescaled to be stochastic again\&. MCL iterands are theoretically known to
-be sparse in a weighted sense, and this manoever effectively perturbs the
-MCL process a little in order to obtain matrices that are genuinely
-sparse, thus keeping the computation tractable\&. An example of monitoring
-pruning can be found in the discussion of
-\fB-v\fP\ \&\fBpruning\fP
-at the end of this section\&.
-
-\fBmcl\fP proceeds as follows\&. First, entries that are smaller than
-\fIcutoff\fP are removed, resulting in a vector with at most
-\fI1/cutoff\fP entries\&. The cutoff can be supplied either by
-\fB-p\fP, or as the inverse value by \fB-P\fP\&. The latter is more
-intuitive, if your intuition is like mine (P stands for precision or pruning)\&.
-The cutoff just described is rigid; it is the same for all vectors\&. The
-\fB--adapt\fP option causes the computation of a
-cutoff that depends on a vector\&'s homogeneity properties, and this option
-may or may not speed up mcl\&.
-
-Second, if the remaining stochastic mass (i\&.e\&. the sum of all remaining
-entries) is less than \fI<pct>\fP/100 and the number of remaining
-entries is less than \fI<r>\fP (as specified by the \fB-R\fP flag),
-\fBmcl\fP will try to regain ground by recovering the largest discarded
-entries\&. The total number of entries is not allowed to grow larger than
-\fI<r>\fP\&.
-If recovery was not necessary, mcl tries to prune the vector further
-down to at most \fIs\fP entries (if applicable), as specified by the
-\fB-S\fP flag\&. If this results in a vector that satisfies the recovery
-condition then recovery is attempted, exactly as described above\&. The
-latter will not occur of course if \fI<r>\fP <= \fI<s>\fP\&.
-
-The default setting is something like \fB-P\fP\ \&\fB4000\fP \fB-S\fP\ \&\fB500\fP
-\fB-R\fP\ \&\fB600\fP\&. Check the \fB-z\fP flag to be sure\&. There is a set
-of precomposed settings, which can be triggered with the
-\fB-scheme\fP\ \&\fIk\fP option\&. \fIk\fP=4 is the default
-scheme; higher values for \fIk\fP result in costlier and more accurate
-computations (vice versa for lower, cheaper, and less accurate)\&.
-The schemes are listed using the \fB--show-schemes\fP option\&. It is
-advisable to use the \fB-scheme\fP option only in interactive mode,
-and to use the explicit expressions when doing batch processing\&. The
-reason is that there is \fIno guarantee whatsoever\fP that the schemes
-will not change between different releases\&. This is because the scheme
-options should reflect good general purpose settings, and it may become
-appararent that other schemes are better\&.
-
-Note that \&'less accurate\&' or \&'more accurate\&' computations may still
-generate the same output clusterings\&. Use \fBclm dist\fP to compare output
-clusterings for different resource parameters\&. Refer to \fBclm\ \&dist\fP
-for a discussion of this issue\&.
-.in -2m
-
-.ZI 2m "\fB-warn-pct\fP <int> (\fIprune warn percentage\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-warn-factor\fP <int> (\fIprune warn factor\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The two options \fB-warn-pct\fP and \fB-warn-factor\fP relate to
-warnings that may be triggered once the \fIinitial\fP pruning of a vector
-is completed\&. The idea is to issue warnings if initial pruning almost
-completely destroys a computed vector, as this may be a sign that the
-pruning parameters should be changed\&. It depends on the mass remaining
-after initial pruning whether a warning will be issued\&. If that mass is
-less than \fIwarn-pct\fP or if the number of remaining entries is smaller
-by a factor \fIwarn-factor\fP than both the number of entries originally
-computed \fIand\fP the recovery number, in that case, \fBmcl\fP will issue a
-warning\&.
-
-\fB-warn-pct\fP takes an integer between 0 and 100 as parameter,
-\fB-warn-factor\fP takes a real positive number\&. They default to
-something like 30 and 50\&.0\&. If you want to see less warnings, decrease
-\fIwarn-pct\fP and increase \fIwarn-factor\fP\&. Set \fIwarn-factor\fP to zero
-if you want no warnings\&.
-.in -2m
-
-.ZI 2m "\fB-v\fP\ \&\fBpruning\fP"
-\&
-.br
-Pruning verbosity mode causes \fBmcl\fP to emit several statistics related to
-the pruning process, each of which is described below\&. Use
-\fB-v\fP\ \&\fBexplain\fP to get explanatory headers in the output as well
-(or simply use \fB-v\fP\ \&\fBall\fP)\&.
-.in -2m
-.SH IMPLEMENTATION OPTIONS
-
-.ZI 2m "\fB-sparse\fP <int> (\fIsparse matrix multiplication threshold\fP)"
-\&
-.br
-This value (by default set to 10) determines when mcl switches to sparse matrix/vector multiplication\&.
-For a given column stochastic vector (corresponding with all the neighbours
-of a given node \fCv\fP according to the current mcl iterand) the sum \fCS\fP of neighbour counts
-of all neighbours of \fCv\fP is computed, counting duplicates\&. This is exactly the
-number of matrix entries involved in the computation of the new column vector
-for the matrix product\&. If \fCS\fP times \fI<int>\fP does not exceed the
-number of nodes in the graph (equal to both column and row dimension of
-the matrices used) then a sparse implementation is used\&. Otherwise
-an optimized regular implementation is used\&. Intuitively, this option can
-be thought of as the estimated overhead per matrix floating point operation incurred
-by the sparse implementation compared with the regular implementation\&.
-MCL uses this estimated overhead to determine which implementation is likely
-to be quicker\&. Testing has shown this strategy works very well for graphs of a wide
-range of sizes, including graphs with up to 3 million nodes and 500 million edges\&.
-
-\fBNOTE\fP
-.br
-The effectiveness of this option is influenced by hardware-specific properties
-such as the CPU L2 cache size\&. The default value should work reasonably well
-across a wide variety of scenarios, but it may be possible to squeeze
-faster run times out of mcl by tuning this parameter to the graphs that are
-specific for your application domain\&.
-.in -2m
-.SH EXAMPLES
-
-The following is an example of label input
-
-.di ZV
-.in 0
-.nf \fC
----8<------8<------8<------8<------8<---
-cat hat 0\&.2
-hat bat 0\&.16
-bat cat 1\&.0
-bat bit 0\&.125
-bit fit 0\&.25
-fit hit 0\&.5
-hit bit 0\&.16
---->8------>8------>8------>8------>8---
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-It can be clustered like this:
-
-.di ZV
-.in 0
-.nf \fC
-mcl cathat --abc -o out\&.cathat
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The file out\&.cathat should now like like this
-
-.di ZV
-.in 0
-.nf \fC
----8<------8<------8<------8<------8<---
-cat hat bat
-bit fit hit
---->8------>8------>8------>8------>8---
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-A few things to note\&. First, MCL will symmetrize any
-arrow it finds\&. If it sees \fCbat cat 1\&.0\fP it will act as if it also
-saw \fCcat bat 1\&.0\fP\&. You can explicitly specify \fCcat bat 1\&.0\fP,
-mcl will in the first parse stage simply end up with duplicate
-entries\&. Second, MCL deduplicates repeated edges by taking the
-one with the maximum value\&. So,
-
-.di ZV
-.in 0
-.nf \fC
----8<------8<------8<------8<------8<---
-cat hat 0\&.2
-hat cat 0\&.16
-hat cat 0\&.8
---->8------>8------>8------>8------>8---
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Will result in two arrows \fCcat-hat\fP and \fChat-cat\fP both
-with value 0\&.8\&.
-.SH APPLICABILITY
-
-\fBmcl\fP will work very well for graphs in which the diameter of the natural
-clusters is not too large\&. The presence of many edges between different
-clusters is not problematic; as long as there is cluster structure, mcl
-will find it\&. It is less likely to work well for graphs with clusters
-(inducing subgraphs) of large diameter, e\&.g\&. grid-like graphs derived from
-Euclidean data\&. So mcl in its canonical form is certainly not fit for
-boundary detection or image segmentation\&. I experimented with a modified
-mcl and boundary detection in the thesis pointed to below (see
-\fBREFERENCES\fP)\&. This was fun and not entirely unsuccesful, but not
-something to be pursued further\&.
-
-\fBmcl\fP likes \fIundirected input graphs best\fP, and it really dislikes graphs
-with node pairs (i,j) for which an arc going from i to j is present and the
-counter-arc from j to i is absent\&. Try to make your input graph undirected\&.
-Furthermore, mcl interprets edge weights in graphs as similarities\&. If you
-are used to working with dissimilarities, you will have to convert those to
-similarities using some conversion formula\&. The most important thing is
-that you feel confident that the similarities are reasonable, i\&.e\&. if X is
-similar to Y with weight 2, and X is similar to Z with weight 200, then this
-should mean that the similarity of Y (to X) is neglectible compared with the
-similarity of Z (to X)\&.
-
-\fBmcl\fP is probably not suited for clustering \fItree graphs\fP\&. This is because
-mcl works best if there are multiple paths between different nodes in the
-natural clusters, but in tree graphs there is only one path between any pair
-of nodes\&. Trees are too sparse a structure for mcl to work on\&.
-
-\fBmcl\fP may well be suited for clustering \fIlattices\fP\&. It will depend
-on the density characteristics of the lattice, and the conditions for
-success are the same as those for clustering graphs in general: The
-diameter of the natural clusters should not be too large\&.
-\fBNOTE\fP when clustering a lattice, you \fIhave\fP to cluster
-the underlying undirected graph, and not the directed graph that represents
-the lattice itself\&. The reason is that one has to allow mcl (or any other
-cluster algorithm) to \&'look back in time\&', so to speak\&. Clustering and
-directionality bite each other (long discussion omitted)\&.
-
-\fBmcl\fP has a worst-case time complexity O(N*k^2), where N is the number of
-nodes in the graph, and k is the maximum number of neighbours tracked during
-computations\&. k depends on the \fB-P\fP and \fB-S\fP options\&. If the
-\fB-S\fP option is used (which is the default setting) then k equals the
-value corresponding with this option\&. Typical values for k are in the range
-500\&.\&.1000\&. The average case is much better than the worst case though, as
-cluster structure itself has the effect of helping mcl\&'s pruning schemes,
-certainly if the diameter of natural clusters is not large\&.
-.SH FILES
-
-There are currently no resource nor configuration files\&.
-The mcl matrix format is described in the \fBmcxio(5)\fP section\&.
-.SH ENVIRONMENT
-
-.ZI 2m "MCLXIODIGITS"
-\&
-.br
-When writing matrices in interchange format, mcl will use this variable (if
-present) as the precision (number of digits) for printing the fractional
-part of values\&.
-.in -2m
-
-.ZI 2m "MCLXIOVERBOSITY"
-\&
-.br
-MCL and its sibling applications will usually report about matrix
-input/output from/to disk\&. The verbosity level can be regulated
-via MCLXIOVERBOSITY\&. These are the levels it can currently be set to\&.
-
-.ZJ 1m 1m "1"
-Silent but applications may alter this\&.
-.in -2m
-.ZJ 1m 1m "2"
-Silent and applications can not alter this\&.
-.in -2m
-.ZJ 1m 1m "4"
-Verbose but applications may alter this\&.
-.in -2m
-.ZJ 1m 1m "8"
-Verbose and applications can not alter this (default)\&.
-.in -2m
-.in -2m
-
-.ZI 2m "MCLXIOFORMAT"
-\&
-.br
-MCL and its sibling applications will by default output matrices
-in interchange format rather than binary format (cf\&. \fBmcxio(5)\fP)\&.
-The desired format can be controlled via the variable
-MCLXIOFORMAT\&. These are the levels it can currently be set to\&.
-
-.ZJ 1m 1m "1"
-Interchange format but applications may alter this\&.
-.in -2m
-.ZJ 1m 1m "2"
-Interchange format and applications can not alter this (default)\&.
-.in -2m
-.ZJ 1m 1m "4"
-Binary format but applications may alter this\&.
-.in -2m
-.ZJ 1m 1m "8"
-Binary format and applications can not alter this\&.
-.in -2m
-.in -2m
-
-.ZI 2m "MCLXICFLAGS"
-\&
-.br
-If matrices are output in interchange format, by default empty vectors
-will not be listed\&. Equivalently (during input time),
-vectors for which no listing is present are understood to be empty -
-note that the \fIpresence\fP of a vector is established using
-the domain information found in the header part\&.
-It is possible to enforce listing of empty vectors by
-setting bit \&'1\&' in the variable MCLXICFLAGS\&.
-.in -2m
-
-.ZI 2m "MCLXIOUNCHECKED"
-\&
-.br
-MCL and its sibling applications will always check a matrix for consistency
-while it is being read\&. If this variable is set, the consistency check is
-omitted\&. For large graphs the speed up can be considerable\&. However, if the
-input graph is not conforming it will likely crash the application that
-is using it\&.
-.in -2m
-.SH DIAGNOSTICS
-
-If \fBmcl\fP issues a diagnostic error, it will most likely be
-because the input matrix could not be parsed succesfully\&.
-\fBmcl\fP tries to be helpful in describing the kind of parse error\&.
-The mcl matrix format is described in the \fBmcxio(5)\fP section\&.
-.SH BUGS
-
-No known bugs at this time\&.
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH HISTORY/CREDITS
-
-The MCL algorithm was conceived in spring 1996 by the present author\&.
-The first implementation of the MCL algorithm followed that spring
-and summer\&. It was written in Perl and proved the viability of
-the algorithm\&. The implementation described here began its life in
-autumn 1997\&. The first versions of the vital matrix library
-were designed jointly by Stijn van Dongen and Annius Groenink in
-the period Oktober 1997 - May 1999\&. The efficient matrix-vector
-multiplication routine was written by Annius\&. This routine is
-without significant changes still one of the cornerstones of this
-MCL implementation\&.
-
-Since May 1999 all MCL libraries have seen much development and
-redesign by the present author\&. Matrix-matrix multiplication has been
-rewritten several times to take full advantage of the sparseness
-properties of the stochastic matrices brought forth by the MCL
-algorithm\&. This mostly concerns the issue of pruning \- removal of
-small elements in a stochastic column in order to keep matrices
-sparse\&.
-
-Very instructive was that around April 2001 Rob Koopman pointed out
-that selecting the k largest elements out of a collection of n is
-best done using a min-heap\&. This was the key to the second major
-rewrite (now counting three) of the MCL pruning schemes, resulting in
-much faster code, generally producing a more accurate computation of
-the MCL process\&.
-
-In May 2001 Anton Enright initiated the parallellization of the
-\fBmcl\fP code and threaded inflation\&. From this example, Stijn threaded
-expansion\&. This was great, as the MCL data structures and operands
-(normal matrix multiplication and Hadamard multiplication) just beg
-for parallellization\&.
-
-Onwards\&.
-The January 2003 03-010 release introduced support for sparsely
-enumerated (i\&.e\&. indices need not be sequential) graphs and matrices, the
-result of a major overhaul of the matrix library and most higher layers\&.
-Conceptually, the library now sees matrices as infinite quadrants
-of which only finite subsections happen to have nonzero entries\&.
-
-The June 2003 03-154 release introduced unix-type pipelines for clustering,
-including the BLAST parser mcxdeblast and the mclblastline script\&.
-The April 2004 04-105 release revived binary format, which has been a first
-class citizen every since\&.
-
-With the March 2005 05-090 release mcxsubs finally acquired a sane
-specification syntax\&. The November 2005 05-314 release brought the ability
-to stream label input directly into mcl\&. The subsequent release introduced a
-transformation language shared by various mcl siblings that allows arbitrary
-progressions of transformations to be applied to either stream values or
-matrix values\&.
-
-Joost van Baal set up the mcl CVS tree and packaged mcl for Debian
-GNU/Linux\&. He completely autotooled the sources, so much so that at first I
-found it hard to find them back amidst bootstrap, aclocal\&.m4, depcomp, and
-other beauties\&.
-
-Jan van der Steen shared his elegant mempool code\&. Philip Lijnzaad gave
-useful comments\&. Philip, Shawn Hoon, Abel Ureta-Vidal,
-and Martin Mokrejs sent helpful bug reports\&.
-
-Abel Ureta-Vidal and Dinakarpandian Deendayal commented on
-and contributed to mcxdeblast and mcxassemble\&.
-
-Tim Hughes contributed several good bug reports for mcxassemble,
-mcxdeblast and zoem (a workhorse for \fBclm format\fP)\&.
-.SH SEE ALSO
-
-\fBmclfaq(7)\fP - Frequently Asked Questions\&.
-
-\fBmcxio(5)\fP - a description of the mcl matrix format\&.
-
-There are many more utilities\&. Consult
-\fBmclfamily(7)\fP for an overview of and links to all the documentation
-and the utilities in the mcl family\&.
-
-\fBminimcl\fP is a 200-line perl implementation of mcl\&. It is shipped
-in the mcl distribution and can be found online at
-http://micans\&.org/mcl\&.
-
-mcl\&'s home at http://micans\&.org/mcl/\&.
-.SH REFERENCES
-
-[1]
-Stijn van Dongen, \fIGraph Clustering by Flow Simulation\fP\&.
-PhD thesis, University of Utrecht, May 2000\&.
-.br
-http://www\&.library\&.uu\&.nl/digiarchief/dip/diss/1895620/inhoud\&.htm
-
-[2]
-Stijn van Dongen, \fIGraph Clustering Via a Discrete Uncoupling Process\fP,
-SIAM Journal on Matrix Analysis and Applications, 30(1):121-141, 2008\&.
-http://link\&.aip\&.org/link/?SJMAEL/30/121/1
-
-[3]
-Stijn van Dongen\&. \fIA cluster algorithm for graphs\fP\&.
-Technical Report INS-R0010, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0010\&.ps\&.Z
-
-[4]
-Stijn van Dongen\&. \fIA stochastic uncoupling process for graphs\fP\&.
-Technical Report INS-R0011, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0011\&.ps\&.Z
-
-[5]
-Stijn van Dongen\&. \fIPerformance criteria for graph clustering and Markov
-cluster experiments\fP\&. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000\&.
-.br
-http://www\&.cwi\&.nl/ftp/CWIreports/INS/INS-R0012\&.ps\&.Z
-
-[6]
-Enright A\&.J\&., Van Dongen S\&., Ouzounis C\&.A\&.
-\fIAn efficient algorithm for large-scale detection of protein families\fP,
-Nucleic Acids Research 30(7):1575-1584 (2002)\&.
-.SH NOTES
-
-This page was generated from \fBZOEM\fP manual macros,
-http://micans\&.org/zoem\&. Both html and roff pages can be created
-from the same source without having to bother with all the usual conversion
-problems, while keeping some level of sophistication in the typesetting\&.
diff --git a/doc/mcl.html b/doc/mcl.html
deleted file mode 100644
index 3bb01f9..0000000
--- a/doc/mcl.html
+++ /dev/null
@@ -1,1522 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
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-<title>The mcl manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcl.ps"><b>mcl</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#started">GETTING STARTED</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#pruneoptions">PRUNING OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#impl">IMPLEMENTATION OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#examples">EXAMPLES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#applicability">APPLICABILITY</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">10.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#files">FILES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">11.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#environment">ENVIRONMENT</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">12.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#diagnostics">DIAGNOSTICS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">13.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#bugs">BUGS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">14.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">15.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#history">HISTORY/CREDITS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">16.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">17.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">18.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#notes">NOTES</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcl — The Markov Cluster Algorithm, aka the MCL algorithm.</p>
-<p style="margin-bottom:0" class="asd_par">
-This program implements <b>mcl</b>, a cluster algorithm for graphs. A single
-parameter controls the granularity of the output clustering, namely the
-<a class="intern" href="#opt-I"><b>-I</b> <i>inflation</i></a> option described further below.
-In standard usage of the program this parameter is the only one that may
-require changing. By default it is set to 2.0 and this is a good way to
-start. If you want to explore cluster structure in graphs with MCL, vary
-this parameter to obtain clusterings at different levels of granularity. A
-good set of starting values is 1.4, 2, 4, and 6.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The program has a rather large set of options. Except for <a class="intern" href="#opt-I"><b>-I</b></a>
-none affects the clustering method itself. The other options are for a
-variety of aspects, such as study of the underlying <span class="smallcaps">MCL</span> process (i.e.
-dumping of iterands), network preprocessing (incorporated for efficiency),
-resource allocation options (for large-scale analyses), output naming
-and placement, output formatting, setting of verbosity levels, and so on.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Network construction and reduction techniques should not be considered as
-part of a clustering algorithm. Nevertheless particular techniques may
-benefit particular methods or applications. In mcl many transformations are
-accessible through the <a class="intern" href="#opt-tf"><b>-tf</b></a> option. It can be used for edge
-weight transformations and selection, as well as transformations that act on
-a graph as a whole.
-It is for example possible to remove edges with weight below 0.7 by issuing
-<b>-tf</b> <b>'gq(0.7)'</b>, where the quotes are necessary to prevent the shell
-from interpreting the parentheses. The option accepts more complicated
-sequences, such as <b>-tf</b> <b>'gq(0.7),add(-0.7)'</b>. This causes all
-remaining edge weights to be shifted to the range [0-0.3], assuming that the
-input contains correlations. Many more transformations are supported, as
-documented in <a class="local sibling" href="mcxio.html">mcxio</a>. Examples of graph-wide transformations are
-<tt>'#knn(<num>)'</tt> and <tt>'#ceilnb(<num>)'</tt>. The first only keeps those edges
-that occur in the list of top-<tt><num></tt> edges of highest weight in both of
-its incident nodes. The second removes edges from nodes of highest degree
-first, proceeding until all node degrees satisfy the given threshold.
-The <a class="intern" href="#opt-pi"><b>-pi</b></a> (pre-inflation) option can be used to increase the
-contrast in edge weights. This may be useful when clusterings are coarse and
-fine-grained clusterings are difficult to obtain.
-</p>
-
-<a name="started"></a>
-<h2>GETTING STARTED</h2>
-<p style="margin-top:0em; margin-bottom:0em">There are two main modes of invocation. The most accessible is
-<i>label mode</i>
-which assumes a format alternatively called label input or <span class="smallcaps">ABC</span>-format.
-The input is then a file or stream in which each
-line encodes an edge in terms of two labels (the 'A' and the 'B')
-and a numerical value (the 'C'), all separated
-by white space. The most basic example of usage is this:
-</p>
-<div class="verbatim"> <b>mcl</b> <-|fname> <a class="intern" href="#opt--abc"><b>--abc</b></a> <a class="intern" href="#opt-o"><b>-o</b> <i>fname-out</i></a></div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output is then a file where each line is a cluster of tab-separated
-labels.
-If clustering is part of a larger workflow where it
-is desirable to analyse and compare multiple clusterings,
-then it is a good idea to use native mode rather than <span class="smallcaps">ABC</span> mode.
-The reason for this is that native mode is understood
-by all programs in the mcl suite. It is a more stringent
-and unambiguous format, and hence more suitable for data exchange.
-The reader is refered to <a class="local sibling" href="clmprotocols.html">clmprotocols</a> for more information.
-</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-The example invocation below assumes matrix input, as explained above
-and described in the <a class="local sibling" href="mcxio.html">mcxio</a> section. Switching to label mode requires
-the input file to be in <span class="smallcaps">ABC</span>-format and the addition of the <a class="intern" href="#opt--abc"><b>--abc</b></a>
-option.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> <-|fname>
-<a class="intern" href="#opt-I"><b>[-I</b> <num> (<i>inflation</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <str> (<i>fname</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-These options are sufficient in 95 percent of the cases or more. The first
-argument must be the name of a file containing a graph/matrix in the mcl
-input format, or a hyphen to read from STDIN. With respect to clustering,
-the <a class="intern" href="#opt-I"><b>-I</b> option</a> is foremost relevant.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The full listing of <b>mcl</b> options is shown further below, separated
-into parts corresponding with functional aspects such
-as clustering, threading, verbosity, network preprocessing, pruning and resource management,
-automatic output naming, and dumping.
-</p>
-<p style="margin-bottom:0"><b>Baseline clustering options</b><br>
-<a class="intern" href="#opt-I"><b>[-I</b> <num> (<i>inflation</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>fname</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Output options</b><br>
-<a class="intern" href="#opt-odir"><b>[-odir</b> <dname> (<i>directory</i>)<b>]</b></a>
-<a class="intern" href="#opt--d"><b>[--d</b> (<i>use input directory for output</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Input options</b><br>
-<a class="intern" href="#opt--abc"><b>[--abc</b> (<i>expect/write labels</i>)<b>]</b></a>
-<a class="intern" href="#opt--sif"><b>[--sif</b> (<i>expect/write labels</i>)<b>]</b></a>
-<a class="intern" href="#opt--etc"><b>[--etc</b> (<i>expect/write labels</i>)<b>]</b></a>
-<a class="intern" href="#opt--expect-values"><b>[--expect-values</b> (<i>sif or etc stream contains values</i>)<b>]</b></a>
-<a class="intern" href="#opt-use-tab"><b>[-use-tab</b> <fname> (<i>use mapping to write</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Transform options</b><br>
-<a class="intern" href="#opt-tf"><b>[-tf</b> <tf-spec> (<i>transform input matrix values</i>)<b>]</b></a>
-<a class="intern" href="#opt-abc-tf"><b>[-abc-tf</b> <tf-spec> (<i>transform input stream values</i>)<b>]</b></a>
-<a class="intern" href="#opt--abc-neg-log10"><b>[--abc-neg-log10</b> (<i>take log10 of stream values, negate sign</i>)<b>]</b></a>
-<a class="intern" href="#opt--abc-neg-log"><b>[--abc-neg-log</b> (<i>take log of stream values, negate sign</i>)<b>]</b></a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>create subgraph on clustering</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Cache options</b><br>
-<a class="intern" href="#opt-write-graph"><b>[-write-graph</b> <fname> (<i>write graph</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-graphx"><b>[-write-graphx</b> <fname> (<i>write transformed graph</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-expanded"><b>[-write-expanded</b> <fname> (<i>write expanded graph</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-limit"><b>[--write-limit</b> (<i>write mcl process limit</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Input manipulation options</b><br>
-<a class="intern" href="#opt-pi"><b>[-pi</b> <num> (<i>pre-inflation</i>)<b>]</b></a>
-<a class="intern" href="#opt-ph"><b>[-ph</b> <num> (<i>pre-inflation, max-bound</i>)<b>]</b></a>
-<a class="intern" href="#opt-if"><b>[-if</b> <num> (<i>start-inflation</i>)<b>]</b></a>
-<a class="intern" href="#opt--discard-loops"><b>[--discard-loops=</b><y/n> (<i>discard y/n loops in input</i>)<b>]</b></a>
-<a class="intern" href="#opt--sum-loops"><b>[--sum-loops</b> (<i>set loops to sum of other arcs weights</i>)<b>]</b></a>
-<a class="intern" href="#opt-c"><b>[-c</b> <num> (<i>reweight loops</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Clustering processing options</b><br>
-<a class="intern" href="#opt-sort"><b>[-sort</b> <str> (<i>sort mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-overlap"><b>[-overlap</b> <str> (<i>overlap mode</i>)<b>]</b></a>
-<a class="intern" href="#opt--force-connected"><b>[--force-connected=</b><y/n> (<i>analyze components</i>)<b>]</b></a>
-<a class="intern" href="#opt--check-connected"><b>[--check-connected=</b><y/n> (<i>analyze components</i>)<b>]</b></a>
-<a class="intern" href="#opt--analyze"><b>[--analyze=</b><y/n> (<i>performance criteria</i>)<b>]</b></a>
-<a class="intern" href="#opt--show-log"><b>[--show-log=</b><y/n> (<i>show log</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Verbosity options</b><br>
-<a class="intern" href="#opt-q"><b>[-q</b> <spec> (<i>log levels</i>)<b>]</b></a>
-<a class="intern" href="#opt-v"><b>[-v</b> <str> (<i>verbosity type on</i>)<b>]</b></a>
-<a class="intern" href="#opt-V"><b>[-V</b> <str> (<i>verbosity type off</i>)<b>]</b></a>
-<a class="intern" href="#opt--show"><b>[--show</b> (<i>print (small) matrices to screen</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Thread options</b><br>
-<a class="intern" href="#opt-te"><b>[-te</b> <int> (<i>#expansion threads</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Output file name and annotation options</b><br>
-<a class="intern" href="#opt-o"><b>[-o</b> <str> (<i>fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-ap"><b>[-ap</b> <str> (<i>use str as file name prefix</i>)<b>]</b></a>
-<a class="intern" href="#opt-aa"><b>[-aa</b> <str> (<i>append str to suffix</i>)<b>]</b></a>
-<a class="intern" href="#opt-az"><b>[-az</b> (<i>show output file name and exit</i>)<b>]</b></a>
-<a class="intern" href="#opt-ax"><b>[-ax</b> (<i>show output suffix and exit</i>)<b>]</b></a>
-<a class="intern" href="#opt-annot"><b>[-annot</b> <str> (<i>dummy annotation option</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Dump options</b><br>
-<a class="intern" href="#opt-dump-interval"><b>[-dump-interval</b> <i:j> (<i>dump interval</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump-modulo"><b>[-dump-modulo</b> <int> (<i>dump modulo</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump-stem"><b>[-dump-stem</b> <stem> (<i>dump file stem</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump"><b>[-dump</b> <str> (<i>type</i>)<b>]</b></a>
-<a class="intern" href="#opt-digits"><b>[-digits</b> <int> (<i>printing precision</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>write matrices in binary format</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Info options</b><br>
-<a class="intern" href="#opt--jury-charter"><b>[--jury-charter</b> (<i>explains jury</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>show version</i>)<b>]</b></a>
-<a class="intern" href="#opt-how-much-ram"><b>[-how-much-ram</b> k (<i>RAM upper bound</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>most important options</i>)<b>]</b></a>
-<a class="intern" href="#opt--help"><b>[--help</b> (<i>one-line description for all options</i>)<b>]</b></a>
-<a class="intern" href="#opt-z"><b>[-z</b> (<i>show current settings</i>)<b>]</b></a>
-<a class="intern" href="#opt-az"><b>[-az</b> (<i>show output file name and exit</i>)<b>]</b></a>
-<a class="intern" href="#opt-ax"><b>[-ax</b> (<i>show output suffix and exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--show-schemes"><b>[--show-schemes</b> (<i>show resource schemes</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Implementation options</b><br>
-<a class="intern" href="#opt-sparse"><b>[-sparse</b> <int> (<i>sparse matrix multiplication threshold</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0"><b>Pruning options</b><br>
-The following options all pertain to the various pruning strategies that can
-be employed by <b>mcl</b>. They are described in the <a class="intern" href="#pruneoptions">PRUNING OPTIONS</a>
-section, accompanied by a description of the mcl pruning strategy.
-If your graphs are huge
-and you have an appetite for tuning, have a look at the following:</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#opt-scheme"><b>[-scheme</b> <int> (<i>resource scheme</i>)<b>]</b></a>
-<a class="intern" href="#opt-resource"><b>[-resource</b> <int> (<i>per-node resource maximum</i>)<b>]</b></a>
-<a class="intern" href="#opt-p"><b>[-p</b> <num> (<i>cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt-P"><b>[-P</b> <int> (<i>1/cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt-S"><b>[-S</b> <int> (<i>selection number</i>)<b>]</b></a>
-<a class="intern" href="#opt-R"><b>[-R</b> <int> (<i>recovery number</i>)<b>]</b></a>
-<a class="intern" href="#opt-pct"><b>[-pct</b> <int> (<i>recover percentage</i>)<b>]</b></a>
-<a class="intern" href="#opt-warn-pct"><b>[-warn-pct</b> <int> (<i>prune warn percentage</i>)<b>]</b></a>
-<a class="intern" href="#opt-warn-factor"><b>[-warn-factor</b> <int> (<i>prune warn factor</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The first argument of <b>mcl</b> must be a file name, but some options are allowed
-to appear as the first argument instead. These are the options that cause
-mcl to print out information of some kind, after which it will gracefully
-exit. The full list of these options is</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#opt-z"><b>-z</b></a>,
-<a class="intern" href="#opt-h"><b>-h</b></a>,
-<a class="intern" href="#opt--help"><b>--help</b></a>,
-<a class="intern" href="#opt--version"><b>--version</b></a>,
-<a class="intern" href="#opt--show-settings"><b>--show-settings</b></a>,
-<a class="intern" href="#opt--show-schemes"><b>--show-schemes</b></a>,
-<a class="intern" href="#opt--jury-charter"><b>--jury-charter</b></a>.
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> implements the <b>MCL algorithm</b>, short for the <b>Markov cluster
-algorithm</b>, a cluster algorithm for graphs developed by Stijn van Dongen at
-the Centre for Mathematics and Computer Science in Amsterdam, the
-Netherlands. The algorithm simulates flow using two simple algebraic
-operations on matrices.
-The inception of this flow process and the theory behind it are
-described elsewhere (see <a class="intern" href="#references">REFERENCES</a>). Frequently asked questions
-are answered in the <a class="local sibling" href="mclfaq.html">mclfaq</a> section.
-The program described here is a fast threaded implementation written by the
-algorithm's creator with contributions by several others. Anton Enright
-co-implemented threading; see the <a class="intern" href="#history">HISTORY/CREDITS</a> section for a complete
-account.
-See the <a class="intern" href="#applicability">APPLICABILITY</a> section for a description of the type of
-graph mcl likes best, and for a qualitative assessment of its speed.
-<b>mcl</b> is accompanied by several other utilities for analyzing clusterings and
-performing matrix and graph operations; see the <a class="intern" href="#seealso">SEE ALSO</a> section.</p>
-<p style="margin-bottom:0" class="asd_par">
-The first argument is the input file name,
-or a single hyphen to read from stdin. The rationale for
-making the name of the input file a fixed parameter is that you typically do
-several runs with different parameters. In command line mode it is
-pleasant if you do not have to skip over an immutable parameter all the
-time.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <a class="intern" href="#opt-I"><b>-I</b> <i>f</i> option</a> is the main control,
-affecting cluster granularity.
-In finding good <b>mcl</b> parameter settings for a particular domain,
-or in finding cluster structure at different levels of granularity,
-one typically runs mcl multiple times for varying values of f (refer
-to the <a class="intern" href="#opt-I"><b>-I</b> <i>inflation</i></a> option for further information).</p>
-<p style="margin-bottom:0" class="asd_par"><b>NOTE</b> <span class="smallcaps">MCL</span> interprets the matrix
-entries or graph edge weights as <b>similarities</b>, and it likes
-<b>undirected input graphs</b> best. It can handle directed graphs, but any
-node pair (i,j) for which w(i,j) is much smaller than w(j,i) or vice versa
-will presumably have a slightly negative effect on the clusterings output by
-mcl. Many such node pairs will have a distinctly negative effect, so try to
-make your input graphs undirected. How your edge weights are computed may
-affect mcl's performance. In protein clustering, one way to go is to
-choose the negated logarithm of the BLAST probabilities (see
-<a class="intern" href="#references">REFERENCES</a>).</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b>'s default parameters should make it quite fast under almost all
-circumstances. Taking default parameters, mcl has been used to generate
-good protein clusters on 133k proteins, taking 10 minutes running time on a
-Compaq ES40 system with four alpha EV6.7 processors. It has been applied
-(with good results) to graphs with two million nodes, and if you have the memory
-(and preferably CPUs as well) nothing should stop you from going further.</p>
-<p style="margin-bottom:0" class="asd_par">
-For large graphs, there are several groups of parameters available for
-tuning the mcl computing process, should it be necessary. The easiest thing
-to do is just vary the <a class="intern" href="#opt-scheme"><b>-scheme</b> option</a>. This
-triggers different settings for the group of pruning parameters
-<a class="intern" href="#opt-P"><b>-p/-P</b>, <b>-R</b>, <b>-S</b>, and
-<b>-pct</b></a>. The default setting corresponds with
-<b>-scheme</b> <b>6</b>.
-When doing multiple mcl runs for the same graphs with different
-<b>-I</b> settings (for obtaining clusterings at different levels
-of granularity), it can be useful to factor out the first bit
-of computation that is common to all runs, by using
-the <a class="intern" href="#opt-write-expanded"><b>-write-expanded</b></a> option one time
-and then using <a class="intern" href="#opt-if"><b>-if</b> <i>inflation</i></a> for each run in the set.
-Whether mcl considers a graph large depends mainly on the graph
-connectivity; a highly connected graph on 50,000 nodes is large to
-mcl (so that you might want to tune resources) whereas a sparsely
-connected graph on 500,000 nodes may be business as usual.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> is a memory munger. Its precise appetite depends on the resource
-settings. You can get a rough (and usually much too pessimistic) upper
-bound for the amount of RAM that is needed by using the
-<a class="intern" href="#opt-how-much-ram"><b>-how-much-ram</b> option</a>. The corresponding
-entry in this manual page contains the simple formula via which the upper
-bound is computed.</p>
-<p style="margin-bottom:0" class="asd_par">
-Other options of interest are the option to specify threads
-<a class="intern" href="#opt-te"><b>-te</b></a>, and the verbosity-related options
-<a class="intern" href="#opt-v"><b>-v</b> and <b>-V</b></a>.
-The actual settings are shown with <b>-z</b>, and for graphs with
-at most 12 nodes or so you can view the MCL matrix iterands on screen
-by supplying <a class="intern" href="#opt--show"><b>--show</b></a> (this may give some
-more feeling).</p>
-<p style="margin-bottom:0" class="asd_par">
-MCL iterands allow a generic interpretation as clusterings as well. The
-clusterings associated with early iterands may contain a fair amount of
-overlap. Refer to the <a class="intern" href="#opt-dump"><b>-dump</b> option</a>, the <a class="local sibling" href="mclfaq.html">mclfaq</a>
-manual, and the <b>clm imac</b> utility (Interpret Matrices As Clusterings).
-Use <b>clm imac</b> only if you have a special reason; the normal usage of <b>mcl</b> is
-to do multiple runs for varying <b>-I</b> parameters and use the
-clusterings output by mcl itself.</p>
-<p style="margin-bottom:0" class="asd_par">
-Under very rare circumstances, <b>mcl</b> might get stuck in a seemingly infinite
-loop. If the number of iterations exceeds a hundred and the <i>chaos</i>
-indicator remains nearly constant (presumably around value 0.37), you can
-force mcl to stop by sending it the ALRM signal (usually done
-by <b>kill -s ALRM</b> <i>pid</i>). It will finish the current
-iteration, and interpret the last iterand as a clustering. Alternatively, you
-can wait and mcl might converge by itself or it will certainly stop after
-10,000 iterations. The
-most probable explanation for such an infinite loop is that the input graph
-contains the flip-flop graph of node size three as a subgraph.</p>
-<p style="margin-bottom:0" class="asd_par">
-The creator of this page feels that manual pages are a valuable resource,
-that online html documentation is also a good thing to have, and
-that info pages are way <i>way</i> ahead of their time. The
-<a class="intern" href="#notes">NOTES</a> section explains how this page was created.</p>
-<p style="margin-bottom:0" class="asd_par">
-In the <a class="intern" href="#options">OPTIONS</a> section options are listed in order of
-importance, with related options grouped together.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-I"></a><b>-I</b> <num> (<i>inflation</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sets the main inflation value to <i><num></i>. This value is the main handle
-for affecting cluster granularity. It is usually chosen somewhere
-in the range [1.2-5.0]. <b>-I</b> <b>5.0</b> will tend to result
-in fine-grained clusterings, and <b>-I</b> <b>1.2</b> will tend to
-result in very coarse grained clusterings. Your mileage will vary
-depending on the characteristics of your data. That is why it is
-a good idea to test the quality and coherency of your clusterings
-using <b>clm dist</b> and <b>clm info</b>. This will most likely reveal that
-certain values of <b>-I</b> are simply not right for your data. The
-<b>clm dist</b> section contains a discussion of how to use the cluster
-validation tools shipped with <b>mcl</b> (see the <a class="intern" href="#seealso">SEE ALSO</a> section).</p>
-<p style="margin-bottom:0" class="asd_par">
-With low values for <b>-I</b>, like <b>-I</b> <b>1.2</b>, you should be
-prepared to use more resources in order to maintain quality of
-clusterings, i.e. increase the argument to the
-<a class="intern" href="#opt-scheme"><b>-scheme</b> option</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-odir"></a><b>-odir</b> <dname> (<i>output directory name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--d"></a><b>--d</b> (<i>use input directory for output</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The default mode of output creation for <b>mcl</b> is to create a file name that
-uses the input file name stripped of any leading path components, augmented
-with a prefix '<tt>out.</tt>' and a suffix encoding pivotal <b>mcl</b> parameters.
-This will usually be the inflation value which is the argument to the <b>-I</b>
-option. By default the output file is written in the current directory.
-For example, if the input is named <tt>data/small.mci</tt> for example and
-inflation is set to three, the output file will be named
-<tt>out.small.mci.I30</tt>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This behaviour can be overridden in various ways. The <b>-o</b> option simply
-specifies the output file name, which may include path components that
-should exist. It is possible to send the clustering to STDOUT by supplying
-<b>-o</b> <b>-</b>. With the <b>-odir</b> <i><dname></i> option <b>mcl</b> constructs the
-output file name as before, but writes the file in the directory <i><dname></i>.
-Finally, the option <b>--d</b> is similar but more specific in that <b>mcl</b>
-will write the output in the directory specified by the path component of
-the input file, that is, the directory in which the input file resides.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If either one of
-<a class="intern" href="#opt--abc"><b>--abc</b></a>, <a class="intern" href="#opt--sif"><b>--sif</b></a>, <a class="intern" href="#opt--etc"><b>--etc</b></a> or
-<a class="intern" href="#opt-use-tab"><b>-use-tab</b> <i>tab-file</i></a> is used the output will be in label format.
-Otherwise the clustering is output in the mcl matrix format; see the <a class="local sibling" href="mcxio.html">mcxio</a>
-section for more information on this. Refer also to the group of options
-discussed at <a class="intern" href="#opt--abc"><b>--abc</b></a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Look at the <a class="intern" href="#opt-ap"><b>-ap</b> <i>prefix</i></a> option and its siblings for the
-automatic naming constructions employed by <b>mcl</b> if the <b>-o</b> option is
-not used.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-c"></a><b>-c</b> <num> (<i>reweight loops</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--sum-loops"></a><b>--sum-loops</b> (<i>set loops to sum of other arcs weights</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-With the <b>-c</b> <i><num></i> option, as the final step of loop computation
-(i.e. after initialization and shadowing) all loop weights are multiplied by
-<b><num></b>, if supplied.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--discard-loops"></a><b>--discard-loops</b>=<y/n> (<i>discard loops in input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-By default <b>mcl</b> will remove any loops that are present in the input. Use
-<b>--discard-loops</b>=<b>n</b> to turn this off. Bear in mind that loops will
-still be modified in all cases where the loop weight is not maximal among
-the list of edge weights for a given node.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--abc"></a><b>--abc</b> (<i>expect/write labels</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--sif"></a><b>--sif</b> (<i>expect/write labels</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--etc"></a><b>--etc</b> (<i>expect/write labels</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--expect-values"></a><b>--expe [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These items all relate to label input and/or label output.
-<b>--abc</b> tells <b>mcl</b> to expect label input and output clusters
-in terms of those labels. This simple format expects two or
-three fields separated by white space on each line.
-The first and second fields are interpreted as labels specifying
-source and destination node respectively. The third field, if present,
-specifies the weight of the arc connecting the two nodes.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The option <b>--sif</b> tells <b>mcl</b> to expect <span class="smallcaps">SIF</span> (Simple Interaction File)
-format. This format is line based. The first two fields
-specify the source node (as a label) and the relationship type. An arbitrary number
-of fields may follow, each containing a label identifying a destination node.
-The second field is simply ignored by <b>mcl</b>.
-As an extension to the SIF format
-weights may optionally follow the labels, separated from them with a colon character.
-It is in this case necessary to use the <b>--expect-values</b> option.
-The <b>--etc</b> option expects a format identical in all respects except
-that the relationship type is not present, so that all fields after the first
-are interpreted as destination labels.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>-use-tab</b> is only useful when matrix input is used.
-It will use the tab file to convert the output to labels; it does
-not fail on indices missing from the tab file, but will bind
-these to generated dummy labels.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-abc-tf"></a><b>-abc-tf</b> <tf-spec> (<i>transform input stream values</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--abc-neg-log10"></a><b>--abc-neg-log10</b> (<i>take log10 of stream values, negate sign</i>)</div [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>-tf</b> transforms the values of the input matrix according
-to <b><tf-spec></b>. <b>-abc-tf</b> transforms the stream values
-(when <a class="intern" href="#opt--abc"><b>--abc</b></a> is used) according to <b><tf-spec></b>.
-<b>--abc-neg-log</b> and <b>--abc-neg-log10</b>
-imply that the stream input values are
-replaced by the negation of their log or log10 values, respectively.
-The reason for their existence is documented in <a class="local sibling" href="mcxio.html">mcxio</a>.
-For a description of the transform language excpected/accepted
-in <b><tf-spec></b> refer to the same.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>create subgraph on clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-bottom:0" class="asd_par">
-With this option <b>mcl</b> will subcluster the provided clustering.
-It does so by removing, first of all, all edges from the input
-graph that connect different clusters.
-The resulting graph consists of different
-components, at least as many as there are clusters in
-the input clustering. This graph is then subjected to transformations,
-if any are specified, and then clustered.
-The output name is constructed by appending the normal mcl-created
-file name suffix to the name of the input clustering.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-graph"></a><b>-write-graph</b> <fname> (<i>write graph</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-graphx"></a><b>-write-graphx</b> <fname> (<i>write transformed graph</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-expanded"></a><b>-write-expanded</b> <fname> (<i>write expanded graph</i>)</div><di [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The first two options are somewhat outdated, in that the prefered way of
-loading networks is by using <a class="local sibling" href="mcxload.html">mcxload</a>. The option
-<b>-write-expanded</b> can be useful for exploring more complicated input
-transformations that incorporate an expansion step, but is not really
-relevant for production use. The last option is mainly educational and for
-analyzing the <b>mcl</b> process itself.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-scheme"></a><b>-scheme</b> <num> (<i>use a preset resource scheme</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-resource"></a><b>-resource</b> <num> (<i>allow n neighbours throughout</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-There are currently seven different resource schemes, indexed 1..7.
-High schemes result in more expensive computations that may possibly be
-more accurate. The default scheme is 4. When <b>mcl</b> is done, it will give a
-grade (the so called <i>jury synopsis</i>) to the appropriateness of the
-scheme used. <i>A low grade does not necessarily imply that the
-resulting clustering is bad</i> - but anyway, a low grade should be reason
-to try for a higher scheme.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Use the <b>-resource</b> <i><num></i> option to cap for each nodes the number of
-neighbours tracked during computation at <i><num></i> nodes.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <a class="intern" href="#pruneoptions">PRUNING OPTIONS</a> section contains an elaborate description
-of the way <b>mcl</b> manages resources, should you be interested.
-In case you are worried about the validation of the resulting
-clusterings, the <a class="local sibling" href="mclfaq.html">mclfaq</a> section
-has several entries discussing this issue. The bottom line is
-that you have to compare the clusterings resulting from different
-schemes (and otherwise identical parameters) using utilities
-such as <b>clm dist</b>, <b>clm info</b> on the one hand, and your
-own sound judgment on the other hand.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If your input graph is extremely dense, with an average node degree
-(i.e. the number of neighbours per node) that is somewhere above
-500, you may need to filter the input graph by removing edges,
-for example by using one of <b>-tf</b> <b>'#ceilnb()'</b>
-or <b>-tf</b> <b>'#knn()'</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--show-schemes"></a><b>--show-schemes</b> (<i>show preset resource schemes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shows the explicit settings to which the different preset schemes
-correspond.</p>
-<p style="margin-bottom:0" class="asd_par">
-The characteristics are written in the same format (more or less) as
-the output triggered by <a class="intern" href="#opt-v-pruning"><b>-v</b> <b>pruning</b></a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-V"></a><b>-V</b> <str> (<i>verbosity type off</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-See the <b>-v</b> option below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-v"></a><b>-v</b> <str> (<i>verbosity type on</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These are the different verbosity modes:</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>pruning</b><br>
-<b>explain</b><br>
-<b>cls</b><br>
-<b>all</b></p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-q"></a><b>-q</b> <spec> (<i>log levels</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-bottom:0" class="asd_par">
-To make mcl as quiet as can be, add
-<b>-q</b> <b>x</b> <b>-V</b> <b>all</b> to the command line.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-q</b> option governs a general logging mechanism.
-The format accepted is described in the <a class="local sibling" href="tingea.log.html">tingea.log</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-The other options govern verbosity levels specific to mcl. <b>-v</b> <b>all</b>
-turns them all on, <b>-V</b> <b>all</b> turns them all off. <b>-v</b> <i>str</i> and
-<b>-V</b> <i>str</i> turn on/off the single mode <i>str</i> (for <i>str</i>
-equal to one of <b>pruning</b>, <b>cls</b>, or <b>explain</b>). Each verbosity
-mode is given its own entry below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>-v</b> <b>explain</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This mode causes the output of explanatory headers illuminating the
-output generated with the <b>pruning</b> verbosity mode.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>-v</b> <b>pruning</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This mode causes output of resource-related quantities. It has
-<a class="intern" href="#opt-v-pruning">a separate entry in the PRUNING OPTIONS section</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>-v</b> <b>cls</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This mode (on by default) prints a terse list of characteristics of the
-clusterings associated with intermediate iterands. The characteristics are
-<b>E/V</b>, <b>cls</b>, <b>olap</b>, and <b>dd</b>. They respectively stand for the
-number of outgoing arcs per node (as an average), the number of clusters in
-the overlapping clustering associated with the iterand, the number of nodes
-in overlap, and the <i>dag depth</i> associated with the DAG (directed acyclic
-graph) associated with the iterand. For more information on this DAG refer
-to the <a class="intern" href="#opt-dump"><b>-dump</b></a> option description in this manual and also
-<a class="local sibling" href="mclfaq.html">mclfaq</a>.</p>
-<p style="margin-bottom:0"><b>Standard log information</b><br></p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " >m-ie</div></div>
-<div class=" item_text " style="margin-left:5em">
-This gives the ratio of (1) the number of edges after initial expansion, before pruning, to
-(2) the number of edges of the current iterand.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >m-ex</div></div>
-<div class=" item_text " style="margin-left:5em">
-This gives the ratio of (1) the number of edges after expansion (including pruning), to
-(2) the number of edges of the current iterand.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >i-ex</div></div>
-<div class=" item_text " style="margin-left:5em">
-This gives the ratio of (1) the number of edges after expansion (including pruning), to
-(2) the number of edges of the original input graph.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >fmv</div></div>
-<div class=" item_text " style="margin-left:5em">
-This gives the percentage of nodes (matrix columns) for which full matrix/vector
-computation was used (as opposed to using a sparse technique).
-</div>
-</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-aa"></a><b>-aa</b> <str> (<i>append <str> to suffix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-See the <b>-ap</b> option below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-ap"></a><b>-ap</b> <str> (<i>use <str> as file name prefix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If the <a class="intern" href="#opt-o"><b>-o</b> <i>fname</i></a> option is not used,
-<b>mcl</b> will create a file name (for writing output to) that
-should uniquely characterize the important parameters used in the
-current invocation of mcl. The default format is <b>out.fname.suf</b>,
-where <b>out</b> is simply the literal string <tt>out</tt>, <b>fname</b> is the
-first argument containing the name of the file (with the graph) to be
-clustered, and where <b>suf</b> is the suffix encoding a set of parameters
-(described further below).</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-ap</b> <i>str</i> option specifies a prefix to use
-rather than <b>out.fname</b> as sketched above.
-However, <b>mcl</b> will interpret the character '=', if present
-in <i>str</i>, as a placeholder for the input file name.</p>
-<p style="margin-bottom:0" class="asd_par">
-If the <b>-aa</b> <i>str</i> option is used, <b>mcl</b> will append
-<b>str</b> to the suffix <b>suf</b> created by itself.
-You can use this if you need to encode some extra information in the
-file name suffix.</p>
-<p style="margin-bottom:0" class="asd_par">
-The suffix is constructed as follows. The <b>-I</b> <i>f</i>
-and <b>-scheme</b> parameter are always encoded.
-Other options, such as <b>-pi</b> <i>f</i> and <b>-knn</b>
-are only encoded if they are used. Any real argument <i>f</i>
-is encoded using <i>exactly one</i> trailing digit behind the decimal
-separator (which itself is not written). The setting <b>-I</b> <b>3.14</b>
-is thus encoded as I31. The <b>-scheme</b> option is encoded using the
-letter 's', all other options mentioned here are encoded as themselves
-(stripped of the hyphen). For example</p>
-<div class="verbatim">mcl small.mci -I 3 -c 2.5 -pi 0.8 -scheme 5</div>
-<p style="margin-top:0em; margin-bottom:0em">
-results in the file name <tt>out.small.mci.I30s5c25pi08</tt>.
-If you want to know beforehand what file name will be produced,
-use the <b>-az</b> option.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-az"></a><b>-az</b> (<i>show output file name and exit</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ax"></a><b>-ax</b> (<i>show output suffix and exit</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-If <b>mcl</b> automatically constructs a file name, it can be helpful to known
-beforehand what that file name will be. Use <b>-az</b> and mcl will
-write the file name to STDOUT and exit. This can be used if mcl is
-integrated into other software for which the automatic creation of
-unique file names is convenient.
-<p style="margin-bottom:0" class="asd_par">
-By default mcl incorporates the input file name into the output file
-name and appends a short suffix describing the most important
-option settings. Use <b>-ax</b> to find out what that suffix is.
-This can be useful in wrapper pipeline scripts such as clxcoarse.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-annot"></a><b>-annot</b> <str> (<i>dummy annotation option</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mcl</b> writes the command line with which it was invoked to the output
-clustering file. Use this option to include any additional
-information. MCL does nothing with this option except copying
-it as just described.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-te"></a><b>-te</b> <int> (<i>#expansion threads</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Threading is useful if you have a multi-processor system. <b>mcl</b> will
-spawn <i>k</i> threads of computation. If these are computed
-in parallel (this depends on the number of CPUs available to the
-mcl process) it will speed up the process accordingly.</p>
-<p style="margin-bottom:0" class="asd_par">
-When threading, it is best not to turn on pruning verbosity
-mode if you are letting mcl run unattended, unless you want to
-scrutinize its output later. This is because it makes <b>mcl</b> run
-somewhat slower, although the difference is not dramatic.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-pi"></a><b>-pi</b> <num> (<i>pre-inflation</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ph"></a><b>-ph</b> <num> (<i>pre-inflation, max-bound</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If used, <b>mcl</b> will apply inflation one time to the input graph
-before entering the main process. This can be useful for
-making the edge weights in a graph either more homogeneous (which
-may result in less granular clusterings) or more heterogeneous
-(which may result in more granular clusterings).
-Homogeneity is achieved for values <i><num></i> less than one,
-heterogeneity for values larger than one.
-Values to try are normally in the range <tt>[2.0,10.0]</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-ph</b> option is special in that it does not rescale
-columns to be stochastic. Instead, it rescales columns so that
-the maximum value found in the column stays the same after
-inflation was applied. There is little significance to this,
-and what little there is is undocumented.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-if"></a><b>-if</b> <num> (<i>start-inflation</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If used, <b>mcl</b> will apply inflation one time to the input graph
-before entering the main process. The difference with
-<b>-pi</b> is that with the latter option mcl may apply
-certain transformations after reading in the matrix such
-as adding or modifying loops. The purpose of
-the <b>-if</b> (mnemonic for <i>inflation-first</i>)
-option is to use it on graphs saved
-with the <a class="intern" href="#opt--write-expanded"><b>--write-expanded</b></a> option and convey
-to mcl that it should not apply those transformations.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-dump-interval"></a><b>-dump-interval</b> <i:j> (<i>dump interval</i>)</div><div class=" item_cascade item_leftalign nowrap" ><b>-dump-interval</b> <i>all</i></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Dump during iterations i..j-1. Use <i>all</i> to dump in all
-iterations. See the <b>-dump</b> <i>str</i> option below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-dump-modulo"></a><b>-dump-modulo</b> <int> (<i>dump i+0..i+<int>..</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sampling rate: select only these iterations in the dump interval.
-See the <b>-dump</b> <i>str</i> option below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-dump-stem"></a><b>-dump-stem</b> <stem> (<i>file stem</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the the stem for file names of dumped
-objects (default <i>mcl</i>). See the <b>-dump</b> <i>str</i> option below.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dump"></a><b>-dump</b> <str> (<i>type</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<i>str</i> is checked for substring occurrences of the following entries.
-Repeated use of <b>-dump</b> is also allowed.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>ite</b><br>
-<b>dag</b><br>
-<b>cls</b><br>
-<b>chr</b><br>
-<b>lines</b><br>
-<b>cat</b></p>
-<p style="margin-bottom:0" class="asd_par">
-<b>lines</b> and <b>cat</b> change the mode of dumping. The first
-changes the dump format to a line based pairwise format rather
-than the default mcl matrix format. The second causes all
-dumped items to be dumped to the default stream used for the
-output clustering, which is appended at the end.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>ite</b> option writes <b>mcl</b> iterands to file. The <b>cls</b>
-option writes clusterings associated with mcl iterands to file.
-These clusters are obtained from a particular directed acyclic graph
-(abbreviated as DAG) associated with each iterand. The <b>dag</b> option
-writes that DAG to file. The DAG can optionally be further
-pruned and then again be interpreted as a
-clustering using <b>clm imac</b>, and <b>clm imac</b> can also
-work with the matrices written using the <b>ite</b> option.
-It should be noted that clusterings associated with intermediate
-iterands may contain overlap, which is interesting in
-many applications. For more information
-refer to <a class="local sibling" href="mclfaq.html">mclfaq</a> and the <a class="intern" href="#references">REFERENCES</a> section below.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>result</b> option dumps the usual MCL clustering.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>chr</b> option says, for each iterand I, to output a matrix C with
-characteristics of I. C has the same number of columns as I. For each
-column k in C, row entry 0 is the diagonal or 'loop' value of column k in
-I <i>after</i> expansion and pruning, and <i>before</i> inflation and
-rescaling. Entry 1 is the loop value <i>after</i> inflation and rescaling.
-Entry 2 is the center of column k (the sum of its entries squared)
-computed <i>after</i> expansion and <i>before</i> pruning, entry 3 is the
-maximum value found in that column at the same time. Entry 4 is the
-amount of mass kept for that column <i>after pruning</i>.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-ds</b> option sets the stem for file names of dumped
-objects (default <i>mcl</i>). The <b>-di</b> and <b>-dm</b>
-options allow a selection of iterands to be made.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-digits"></a><b>-digits</b> <int> (<i>printing precision</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This has two completely different uses. It sets
-the number of decimals used for pretty-printing <b>mcl</b> iterands
-when using the <a class="intern" href="#opt--show"><b>--show</b> option</a> (see below),
-and it sets the number of decimals used for writing
-the expanded matrix when using the <a class="intern" href="#opt-write-expanded"><b>-write-expanded</b></a> option.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--show"></a><b>--show</b> (<i>print matrices to screen</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Print matrices to screen. The number of significant digits to be
-printed can be tuned with <b>-digits</b> <i>n</i>. An 80-column screen
-allows graphs (matrices) of size up to 12(x12) to be printed with
-three digits precision (behind the comma), and of size up to 14(x14)
-with two digits. This can give you an idea of how <b>mcl</b> operates,
-and what the effect of pruning is.
-Use e.g. <b>-S</b> <b>6</b> for such
-a small graph and view the MCL matrix iterands with <b>--show</b>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--write-binary"></a><b>--write-binary</b> (<i>output format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write matrix dump output in binary mcl format rather
-than interchange mcl format (the default). Note that <b>mcxconvert</b>
-can be used to convert each one into the other.
-See <a class="local sibling" href="mcxio.html">mcxio</a> and <a class="local sibling" href="mcx.html">mcx</a> for more information.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sort"></a><b>-sort</b> <str> (<i>sort mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<i>str</i> can be one of <b>lex</b>, <b>size</b>, <b>revsize</b>,
-or <b>none</b>. The default is 'revsize', in which the largest
-clusters come first. If the mode is 'size', smallest clusters
-come first, if the mode is 'lex', clusters are ordered
-lexicographically, and if the mode is 'none', the order
-is the same as produced by the procedure used by mcl to
-map matrices onto clusterings.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-overlap"></a><b>-overlap</b> <str> (<i>overlap mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Mode <i>keep</i> causes mcl to retain overlap should this improbable event
-occur. In theory, <b>mcl</b> may generate a clustering that contains overlap,
-although this almost never happens in practice, as it requires some
-particular type of symmetry to be present in the input graph (not just any
-symmetry will do). Mathematically speaking, this is a conjecture and not a
-theorem, but the present author wil eat his shoe if it fails to be true (for
-marzipan values of shoe). It is easy though to construct an input graph for
-which certain mcl settings result in overlap - for example a line graph on
-an odd number of nodes. The default is to excise overlapping parts and
-introduce them as clusters in their own right. It is possible to allocate
-nodes in overlap to the first cluster in which they occur (i.e. rather
-arbitrarily), corresponding with mode <i>cut</i>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-In mode <i>split</i> mcl will put all nodes in overlap into
-separate clusters. These clusters are chosen such that
-two nodes are put in the same new cluster if and only if
-they always occur paired in the clusters of the
-overlapping clustering.</p>
-<p style="margin-bottom:0" class="asd_par">
-This option has no effect on the clusterings that are
-output when using <a class="intern" href="#opt-dump"><b>-dump</b> <i>cls</i></a> -
-the default for those is that overlap is not touched,
-and this default can not yet be overridden.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--force-connected"></a><b>--force-connected</b>=<y/n> (<i>analyze components</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--check-connected"></a><b>--check-connected</b>=<y/n> (<i>analyze components</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If the input graph has strong bipartite characteristics,
-mcl may yield clusters that do not correspond to connected
-components in the input graph. Turn one of these modes on to
-analyze the resultant clustering.</p>
-<p style="margin-bottom:0" class="asd_par">
-If loose clusters are found
-they will be split into subclusters corresponding to
-connected components.
-With <b>--force-connected</b>=<i>y</i> mcl will write the
-corrected clustering to the normal output file, and the old clustering
-to the same file with suffix <tt>orig</tt>.
-With <b>--check-connected</b>=<i>y</i> mcl will write the
-loose clustering to the normal output file, and the corrected clustering
-to the same file with suffix <tt>coco</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-These options are not on by default, as the analysis
-is currently (overly) time-consuming
-and mcl's behaviour actually makes some sense
-(when taking bipartite characteristics into account).</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--analyze"></a><b>--analyze</b>=<y/n> (<i>performance criteria</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-With this mode turned on, <b>mcl</b> will reread the input matrix
-and compute a few performance criteria and attach them to
-the output file. Off by default.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--show-log"></a><b>--show-log</b>=<y/n> (<i>show log</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shows the log with process characteristics on STDOUT.
-By default, this mode is off.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--jury-charter"></a><b>--jury-charter</b> (<i>explains jury</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Explains how the jury synopsis is computed from the jury marks.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--version"></a><b>--version</b> (<i>show version</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Show version.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-how-much-ram"></a><b>-how-much-ram</b> <int> (<i>RAM upper bound</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b><int></b> is interpreted as the number of nodes of an input graph.
-mcl will print the maximum amount of RAM it needs for its computations.
-The formula for this number in bytes is:</p>
-<div class="verbatim"> 2 * c * k * <int>
-
- 2 : two matrices are concurrently held in memory.
- c : mcl cell size (as shown by -z).
- <int>: graph cardinality (number of nodes).
- k : MAX(s, r).
- s : select number (-S, -scheme options).
- r : recover number (-R, -scheme options).</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This estimate will usually be too pessimistic. It does assume though that
-the average node degree of the input graph does not exceed k. The
-<b>-how-much-ram</b> option takes other command-line arguments into
-account (such as <b>-S</b> and <b>-R</b>), and it expresses the
-amount of RAM in megabyte units.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-h"></a><b>-h</b> (<i>show help</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shows a selection of the most important <b>mcl</b> options.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--help"></a><b>--help</b> (<i>show help</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Gives a one-line description for all options.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-z"></a><b>-z</b> (<i>show settings</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Show current settings for tunable parameters.
-<b>--show-settings</b> is a synonym.</p>
-</div>
-</div>
-
-<a name="pruneoptions"></a>
-<h2>PRUNING OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade item_leftalign nowrap" ><a name="opt-p"></a><b>-p</b> <num> (<i>cutoff</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-P"></a><b>-P</b> <int> (<i>1/cutoff</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-S"></a><b>-S</b> <int> (<i>selection number</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-R"></a><b>-R</b> <int> (<i>recover number</i>)</div><div class=" item_ca [...]
-<div class=" item_text " style="margin-left:2em">
-After computing a new (column stochastic) matrix vector during expansion
-(which is matrix multiplication c.q. squaring), the vector is
-successively exposed to different pruning strategies. The intent of
-pruning is that many small entries are removed while retaining much of
-the stochastic mass of the original vector. After pruning, vectors are
-rescaled to be stochastic again. MCL iterands are theoretically known to
-be sparse in a weighted sense, and this manoever effectively perturbs the
-MCL process a little in order to obtain matrices that are genuinely
-sparse, thus keeping the computation tractable. An example of monitoring
-pruning can be found in the discussion of
-<a class="intern" href="#opt-v-pruning"><b>-v</b> <b>pruning</b></a>
-at the end of this section.
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> proceeds as follows. First, entries that are smaller than
-<i>cutoff</i> are removed, resulting in a vector with at most
-<i>1/cutoff</i> entries. The cutoff can be supplied either by
-<b>-p</b>, or as the inverse value by <b>-P</b>. The latter is more
-intuitive, if your intuition is like mine (P stands for precision or pruning).
-The cutoff just described is rigid; it is the same for all vectors. The
-<a class="intern" href="#opt--adapt"><b>--adapt</b> option</a> causes the computation of a
-cutoff that depends on a vector's homogeneity properties, and this option
-may or may not speed up mcl.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Second, if the remaining stochastic mass (i.e. the sum of all remaining
-entries) is less than <i><pct></i>/100 and the number of remaining
-entries is less than <i><r></i> (as specified by the <b>-R</b> flag),
-<b>mcl</b> will try to regain ground by recovering the largest discarded
-entries. The total number of entries is not allowed to grow larger than
-<i><r></i>.
-If recovery was not necessary, mcl tries to prune the vector further
-down to at most <i>s</i> entries (if applicable), as specified by the
-<b>-S</b> flag. If this results in a vector that satisfies the recovery
-condition then recovery is attempted, exactly as described above. The
-latter will not occur of course if <i><r></i> <= <i><s></i>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The default setting is something like <b>-P</b> <b>4000</b> <b>-S</b> <b>500</b>
-<b>-R</b> <b>600</b>. Check the <b>-z</b> flag to be sure. There is a set
-of precomposed settings, which can be triggered with the
-<a class="intern" href="#opt-scheme"><b>-scheme</b> <i>k</i> option</a>. <i>k</i>=4 is the default
-scheme; higher values for <i>k</i> result in costlier and more accurate
-computations (vice versa for lower, cheaper, and less accurate).
-The schemes are listed using the <b>--show-schemes</b> option. It is
-advisable to use the <b>-scheme</b> option only in interactive mode,
-and to use the explicit expressions when doing batch processing. The
-reason is that there is <i>no guarantee whatsoever</i> that the schemes
-will not change between different releases. This is because the scheme
-options should reflect good general purpose settings, and it may become
-appararent that other schemes are better.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Note that 'less accurate' or 'more accurate' computations may still
-generate the same output clusterings. Use <b>clm dist</b> to compare output
-clusterings for different resource parameters. Refer to <a class="local sibling" href="clmdist.html">clm dist</a>
-for a discussion of this issue.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-warn-pct"></a><b>-warn-pct</b> <int> (<i>prune warn percentage</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-warn-factor"></a><b>-warn-factor</b> <int> (<i>prune warn factor</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-The two options <b>-warn-pct</b> and <b>-warn-factor</b> relate to
-warnings that may be triggered once the <i>initial</i> pruning of a vector
-is completed. The idea is to issue warnings if initial pruning almost
-completely destroys a computed vector, as this may be a sign that the
-pruning parameters should be changed. It depends on the mass remaining
-after initial pruning whether a warning will be issued. If that mass is
-less than <i>warn-pct</i> or if the number of remaining entries is smaller
-by a factor <i>warn-factor</i> than both the number of entries originally
-computed <i>and</i> the recovery number, in that case, <b>mcl</b> will issue a
-warning.
-<p style="margin-bottom:0" class="asd_par">
-<b>-warn-pct</b> takes an integer between 0 and 100 as parameter,
-<b>-warn-factor</b> takes a real positive number. They default to
-something like 30 and 50.0. If you want to see less warnings, decrease
-<i>warn-pct</i> and increase <i>warn-factor</i>. Set <i>warn-factor</i> to zero
-if you want no warnings.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-v-pruning"></a><b>-v</b> <b>pruning</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-Pruning verbosity mode causes <b>mcl</b> to emit several statistics related to
-the pruning process, each of which is described below. Use
-<b>-v</b> <b>explain</b> to get explanatory headers in the output as well
-(or simply use <b>-v</b> <b>all</b>).
-</div>
-</div>
-
-<a name="impl"></a>
-<h2>IMPLEMENTATION OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sparse"></a><b>-sparse</b> <int> (<i>sparse matrix multiplication threshold</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This value (by default set to 10) determines when mcl switches to sparse matrix/vector multiplication.
-For a given column stochastic vector (corresponding with all the neighbours
-of a given node <tt>v</tt> according to the current mcl iterand) the sum <tt>S</tt> of neighbour counts
-of all neighbours of <tt>v</tt> is computed, counting duplicates. This is exactly the
-number of matrix entries involved in the computation of the new column vector
-for the matrix product. If <tt>S</tt> times <i><int></i> does not exceed the
-number of nodes in the graph (equal to both column and row dimension of
-the matrices used) then a sparse implementation is used. Otherwise
-an optimized regular implementation is used. Intuitively, this option can
-be thought of as the estimated overhead per matrix floating point operation incurred
-by the sparse implementation compared with the regular implementation.
-MCL uses this estimated overhead to determine which implementation is likely
-to be quicker. Testing has shown this strategy works very well for graphs of a wide
-range of sizes, including graphs with up to 3 million nodes and 500 million edges.
-</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-The effectiveness of this option is influenced by hardware-specific properties
-such as the CPU L2 cache size. The default value should work reasonably well
-across a wide variety of scenarios, but it may be possible to squeeze
-faster run times out of mcl by tuning this parameter to the graphs that are
-specific for your application domain.
-</p>
-</div>
-</div>
-
-<a name="examples"></a>
-<h2>EXAMPLES</h2>
-<p style="margin-bottom:0" class="asd_par">The following is an example of label input</p>
-<div class="verbatim">---8<------8<------8<------8<------8<---
-cat hat 0.2
-hat bat 0.16
-bat cat 1.0
-bat bit 0.125
-bit fit 0.25
-fit hit 0.5
-hit bit 0.16
---->8------>8------>8------>8------>8---</div>
-<p style="margin-top:0em; margin-bottom:0em">It can be clustered like this:</p>
-<div class="verbatim">mcl cathat --abc -o out.cathat</div>
-<p style="margin-top:0em; margin-bottom:0em">The file out.cathat should now like like this</p>
-<div class="verbatim">---8<------8<------8<------8<------8<---
-cat hat bat
-bit fit hit
---->8------>8------>8------>8------>8---</div>
-<p style="margin-top:0em; margin-bottom:0em">A few things to note. First, MCL will symmetrize any
-arrow it finds. If it sees <tt>bat cat 1.0</tt> it will act as if it also
-saw <tt>cat bat 1.0</tt>. You can explicitly specify <tt>cat bat 1.0</tt>,
-mcl will in the first parse stage simply end up with duplicate
-entries. Second, MCL deduplicates repeated edges by taking the
-one with the maximum value. So,</p>
-<div class="verbatim">---8<------8<------8<------8<------8<---
-cat hat 0.2
-hat cat 0.16
-hat cat 0.8
---->8------>8------>8------>8------>8---</div>
-<p style="margin-top:0em; margin-bottom:0em">Will result in two arrows <tt>cat-hat</tt> and <tt>hat-cat</tt> both
-with value 0.8.</p>
-
-<a name="applicability"></a>
-<h2>APPLICABILITY</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> will work very well for graphs in which the diameter of the natural
-clusters is not too large. The presence of many edges between different
-clusters is not problematic; as long as there is cluster structure, mcl
-will find it. It is less likely to work well for graphs with clusters
-(inducing subgraphs) of large diameter, e.g. grid-like graphs derived from
-Euclidean data. So mcl in its canonical form is certainly not fit for
-boundary detection or image segmentation. I experimented with a modified
-mcl and boundary detection in the thesis pointed to below (see
-<a class="intern" href="#references">REFERENCES</a>). This was fun and not entirely unsuccesful, but not
-something to be pursued further.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> likes <i>undirected input graphs best</i>, and it really dislikes graphs
-with node pairs (i,j) for which an arc going from i to j is present and the
-counter-arc from j to i is absent. Try to make your input graph undirected.
-Furthermore, mcl interprets edge weights in graphs as similarities. If you
-are used to working with dissimilarities, you will have to convert those to
-similarities using some conversion formula. The most important thing is
-that you feel confident that the similarities are reasonable, i.e. if X is
-similar to Y with weight 2, and X is similar to Z with weight 200, then this
-should mean that the similarity of Y (to X) is neglectible compared with the
-similarity of Z (to X).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> is probably not suited for clustering <i>tree graphs</i>. This is because
-mcl works best if there are multiple paths between different nodes in the
-natural clusters, but in tree graphs there is only one path between any pair
-of nodes. Trees are too sparse a structure for mcl to work on.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> may well be suited for clustering <i>lattices</i>. It will depend
-on the density characteristics of the lattice, and the conditions for
-success are the same as those for clustering graphs in general: The
-diameter of the natural clusters should not be too large.
-<b>NOTE</b> when clustering a lattice, you <i>have</i> to cluster
-the underlying undirected graph, and not the directed graph that represents
-the lattice itself. The reason is that one has to allow mcl (or any other
-cluster algorithm) to 'look back in time', so to speak. Clustering and
-directionality bite each other (long discussion omitted).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> has a worst-case time complexity O(N*k^2), where N is the number of
-nodes in the graph, and k is the maximum number of neighbours tracked during
-computations. k depends on the <b>-P</b> and <b>-S</b> options. If the
-<b>-S</b> option is used (which is the default setting) then k equals the
-value corresponding with this option. Typical values for k are in the range
-500..1000. The average case is much better than the worst case though, as
-cluster structure itself has the effect of helping mcl's pruning schemes,
-certainly if the diameter of natural clusters is not large.
-</p>
-
-<a name="files"></a>
-<h2>FILES</h2>
-<p style="margin-bottom:0" class="asd_par">
-There are currently no resource nor configuration files.
-The mcl matrix format is described in the <a class="local sibling" href="mcxio.html">mcxio</a> section.
-</p>
-
-<a name="environment"></a>
-<h2>ENVIRONMENT</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " >MCLXIODIGITS</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-When writing matrices in interchange format, mcl will use this variable (if
-present) as the precision (number of digits) for printing the fractional
-part of values.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >MCLXIOVERBOSITY</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-MCL and its sibling applications will usually report about matrix
-input/output from/to disk. The verbosity level can be regulated
-via MCLXIOVERBOSITY. These are the levels it can currently be set to.</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">1</div></div>
-<div class=" item_text " style="margin-left:2em">
-Silent but applications may alter this.
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">2</div></div>
-<div class=" item_text " style="margin-left:2em">
-Silent and applications can not alter this.
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">4</div></div>
-<div class=" item_text " style="margin-left:2em">
-Verbose but applications may alter this.
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">8</div></div>
-<div class=" item_text " style="margin-left:2em">
-Verbose and applications can not alter this (default).
-</div>
-</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >MCLXIOFORMAT</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-MCL and its sibling applications will by default output matrices
-in interchange format rather than binary format (cf. <a class="local sibling" href="mcxio.html">mcxio</a>).
-The desired format can be controlled via the variable
-MCLXIOFORMAT. These are the levels it can currently be set to.</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">1</div></div>
-<div class=" item_text " style="margin-left:2em">
-Interchange format but applications may alter this.
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">2</div></div>
-<div class=" item_text " style="margin-left:2em">
-Interchange format and applications can not alter this (default).
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">4</div></div>
-<div class=" item_text " style="margin-left:2em">
-Binary format but applications may alter this.
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em">8</div></div>
-<div class=" item_text " style="margin-left:2em">
-Binary format and applications can not alter this.
-</div>
-</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >MCLXICFLAGS</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If matrices are output in interchange format, by default empty vectors
-will not be listed. Equivalently (during input time),
-vectors for which no listing is present are understood to be empty -
-note that the <i>presence</i> of a vector is established using
-the domain information found in the header part.
-It is possible to enforce listing of empty vectors by
-setting bit '1' in the variable MCLXICFLAGS.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >MCLXIOUNCHECKED</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-MCL and its sibling applications will always check a matrix for consistency
-while it is being read. If this variable is set, the consistency check is
-omitted. For large graphs the speed up can be considerable. However, if the
-input graph is not conforming it will likely crash the application that
-is using it.</p>
-</div>
-</div>
-
-<a name="diagnostics"></a>
-<h2>DIAGNOSTICS</h2>
-<p style="margin-bottom:0" class="asd_par">
-If <b>mcl</b> issues a diagnostic error, it will most likely be
-because the input matrix could not be parsed succesfully.
-<b>mcl</b> tries to be helpful in describing the kind of parse error.
-The mcl matrix format is described in the <a class="local sibling" href="mcxio.html">mcxio</a> section.</p>
-
-<a name="bugs"></a>
-<h2>BUGS</h2>
-<p style="margin-bottom:0" class="asd_par">
-No known bugs at this time.</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="history"></a>
-<h2>HISTORY/CREDITS</h2>
-<p style="margin-bottom:0" class="asd_par">
-The MCL algorithm was conceived in spring 1996 by the present author.
-The first implementation of the MCL algorithm followed that spring
-and summer. It was written in Perl and proved the viability of
-the algorithm. The implementation described here began its life in
-autumn 1997. The first versions of the vital matrix library
-were designed jointly by Stijn van Dongen and Annius Groenink in
-the period Oktober 1997 - May 1999. The efficient matrix-vector
-multiplication routine was written by Annius. This routine is
-without significant changes still one of the cornerstones of this
-MCL implementation.</p>
-<p style="margin-bottom:0" class="asd_par">
-Since May 1999 all MCL libraries have seen much development and
-redesign by the present author. Matrix-matrix multiplication has been
-rewritten several times to take full advantage of the sparseness
-properties of the stochastic matrices brought forth by the MCL
-algorithm. This mostly concerns the issue of pruning — removal of
-small elements in a stochastic column in order to keep matrices
-sparse.</p>
-<p style="margin-bottom:0" class="asd_par">
-Very instructive was that around April 2001 Rob Koopman pointed out
-that selecting the k largest elements out of a collection of n is
-best done using a min-heap. This was the key to the second major
-rewrite (now counting three) of the MCL pruning schemes, resulting in
-much faster code, generally producing a more accurate computation of
-the MCL process.</p>
-<p style="margin-bottom:0" class="asd_par">
-In May 2001 Anton Enright initiated the parallellization of the
-<b>mcl</b> code and threaded inflation. From this example, Stijn threaded
-expansion. This was great, as the MCL data structures and operands
-(normal matrix multiplication and Hadamard multiplication) just beg
-for parallellization.</p>
-<p style="margin-bottom:0" class="asd_par">
-Onwards.
-The January 2003 03-010 release introduced support for sparsely
-enumerated (i.e. indices need not be sequential) graphs and matrices, the
-result of a major overhaul of the matrix library and most higher layers.
-Conceptually, the library now sees matrices as infinite quadrants
-of which only finite subsections happen to have nonzero entries.</p>
-<p style="margin-bottom:0" class="asd_par">
-The June 2003 03-154 release introduced unix-type pipelines for clustering,
-including the BLAST parser mcxdeblast and the mclblastline script.
-The April 2004 04-105 release revived binary format, which has been a first
-class citizen every since.</p>
-<p style="margin-bottom:0" class="asd_par">
-With the March 2005 05-090 release mcxsubs finally acquired a sane
-specification syntax. The November 2005 05-314 release brought the ability
-to stream label input directly into mcl. The subsequent release introduced a
-transformation language shared by various mcl siblings that allows arbitrary
-progressions of transformations to be applied to either stream values or
-matrix values.</p>
-<p style="margin-bottom:0" class="asd_par">
-Joost van Baal set up the mcl CVS tree and packaged mcl for Debian
-GNU/Linux. He completely autotooled the sources, so much so that at first I
-found it hard to find them back amidst bootstrap, aclocal.m4, depcomp, and
-other beauties.</p>
-<p style="margin-bottom:0" class="asd_par">
-Jan van der Steen shared his elegant mempool code. Philip Lijnzaad gave
-useful comments. Philip, Shawn Hoon, Abel Ureta-Vidal,
-and Martin Mokrejs sent helpful bug reports.</p>
-<p style="margin-bottom:0" class="asd_par">
-Abel Ureta-Vidal and Dinakarpandian Deendayal commented on
-and contributed to mcxdeblast and mcxassemble.</p>
-<p style="margin-bottom:0" class="asd_par">
-Tim Hughes contributed several good bug reports for mcxassemble,
-mcxdeblast and zoem (a workhorse for <b>clm format</b>).</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfaq.html">mclfaq</a> - Frequently Asked Questions.</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a> - a description of the mcl matrix format.</p>
-<p style="margin-bottom:0" class="asd_par">
-There are many more utilities. Consult
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of and links to all the documentation
-and the utilities in the mcl family.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>minimcl</b> is a 200-line perl implementation of mcl. It is shipped
-in the mcl distribution and can be found online at
-<a class="extern" href="http://micans.org/mcl">http://micans.org/mcl</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-mcl's home at <a class="extern" href="http://micans.org/mcl/">http://micans.org/mcl/</a>.</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a name="gcbfs">[1]</a>
-Stijn van Dongen, <i>Graph Clustering by Flow Simulation</i>.
-PhD thesis, University of Utrecht, May 2000.<br>
-<a class="extern" href="http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm">http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="gcvdup">[2]</a>
-Stijn van Dongen, <i>Graph Clustering Via a Discrete Uncoupling Process</i>,
-SIAM Journal on Matrix Analysis and Applications, 30(1):121-141, 2008.
-<a class="extern" href="http://link.aip.org/link/?SJMAEL/30/121/1">http://link.aip.org/link/?SJMAEL/30/121/1</a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="cafg">[3]</a>
-Stijn van Dongen. <i>A cluster algorithm for graphs</i>.
-Technical Report INS-R0010, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="supfg">[4]</a>
-Stijn van Dongen. <i>A stochastic uncoupling process for graphs</i>.
-Technical Report INS-R0011, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="pcfgcmce">[5]</a>
-Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="eaflsdopf">[6]</a>
-Enright A.J., Van Dongen S., Ouzounis C.A.
-<i>An efficient algorithm for large-scale detection of protein families</i>,
-Nucleic Acids Research 30(7):1575-1584 (2002).</p>
-
-<a name="notes"></a>
-<h2>NOTES</h2>
-<p style="margin-bottom:0" class="asd_par">
-This page was generated from <b>ZOEM</b> manual macros,
-<a class="extern" href="http://micans.org/zoem">http://micans.org/zoem</a>. Both html and roff pages can be created
-from the same source without having to bother with all the usual conversion
-problems, while keeping some level of sophistication in the typesetting.
-<a class="local" href="mcl.ps">This</a> is the PostScript derived from the zoem troff
-output.</p>
-</body>
-</html>
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-<title>The mclblastline manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclblastline.ps"><b>mclblastline</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#examples">EXAMPLES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#sealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclblastline — a pipeline for clustering from BLAST files.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mclblastline</b> file-name</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclblastline</b> [deblast options] [pipeline options] file-name</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-<b>mcl</b> has acquired the ability to proceed from label input
-as produced by <b>mcxdeblast</b>. This enables a very lightweight
-mechanism of generating clusterings from BLAST files.
-You might want to use this mechanism,
-documented in the <a class="local sibling" href="mcl.html">mcl manual</a>.</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-mclblastline used to require (given default parameters)
-the presence of the <b>zoem</b> macro processor to produce detailed output.
-This is no longer the case. By default mclblastline now creates
-a line-based tab-separated dump file.
-Zoem <i>will</i> be invoked when the --fmt-fancy option is supplied.
-In that case, zoem obviously has to be installed.</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mclblastline</b> wraps around <b>mclpipeline</b>. It supplies the
-<b>--parser</b>=<i>app</i>
-and <b>--parser-tag</b>=<i>str</i> options, setting them respectively
-to <i>mcxdeblast</i> and <i>blast</i>. This tells
-<a class="local sibling" href="mclpipeline.html">mclpipeline</a> to use
-<a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> as the parse script in its pipeline.
-The significance of
-the <i>blast</i> tag is that any mcxdeblast option can be passed through
-mclblastline and mclpipeline by inserting this tag into the option.
-For example, mcxdeblast accepts the <b>--score</b>=<i>x</i> option.
-When using mclblastline, you specify it as <b>--blast-score</b>=<i>x</i>.
-There are two exceptions to this rule, namely the
-<b>--xi-dat</b>=<i>str</i> and <b>--xo-dat</b>=<i>str</i> options. Refer to
-the <a class="local sibling" href="mclpipeline.html">mclpipeline</a> manual for more information.</p>
-<p style="margin-bottom:0" class="asd_par">
-Additionally, all mclpipeline options are acceptable to <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> as
-well. The <b>--whatif</b> is useful for getting a feel for the pipeline.
-The <b>--mcl-I</b>=<i>f</i> inflation option and <b>--mcl-scheme</b>=<i>i</i> scheme
-index options are your basic means for respectively manipulating cluster
-granularity and allocating resources. Read the <a class="local sibling" href="mcl.html">mcl</a> manual entries for
-a description of the corresponding <b>-I</b> and <b>-scheme</b> mcl
-options.</p>
-<p style="margin-bottom:0" class="asd_par">
-The best advice is to glance over the <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> and <a class="local sibling" href="mclpipeline.html">mclpipeline</a>
-options in order to get a feeling for which of those may come in handy for
-you. Then start experimenting. Use the <b>--whatif</b> option, it will
-tell you what would happen without actually doing it.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-All <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> and <a class="local sibling" href="mclpipeline.html">mclpipeline</a> options.
-mcxdeblast options must be passed using the mechanism described above.</p>
-
-<a name="examples"></a>
-<h2>EXAMPLES</h2>
-<div class="verbatim"> mclblastline --blast-score=b
- --blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This will use bit scores, sort cluster indices such that the corresponding
-labels are ordered alphabetically, ignore bit scores not exceeding 5, and
-use inflation value 2.5. In this case, the output clustering will be in the
-file named <tt>myblastfile.I25s2</tt> (I25 identifying the inflation value and s2
-identifying the resource scheme) and the formatted output will be in the
-file <tt>myblastfile.I25s2.fmt</tt>.</p>
-<div class="verbatim"> mclblastline --prepare-mcl myblastfile
- mclblastline --start-mcl --mcl-I=1.2 myblastfile
- mclblastline --start-mcl --mcl-I=1.6 myblastfile
- mclblastline --start-mcl --mcl-I=2.0 myblastfile
- mclblastline --start-mcl --mcl-I=2.4 myblastfile
- mclblastline --start-mcl --mcl-I=2.8 myblastfile
- etc ..</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The first run prepares an input matrix to be read by <b>mcl</b>.
-In this case its file will be named <tt>myblastfile.sym</tt>.
-The subsequent runs use this matrix.
-<b>CAVEAT</b> there are some options that you need to repeat
-when executing such a resumed run. They are clearly marked
-in the <a class="local sibling" href="mclpipeline.html">mclpipeline</a> manual - namely those options
-that affect names of (intermediate) files. Most importantly,
-this concerns the mclpipeline options that have prefix
-<b>--xo</b> or <b>--xi</b>. For example,</p>
-<div class="verbatim"> mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1.2 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1.6 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.0 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.4 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.8 myblastfile
- etc ..</div>
-<p style="margin-bottom:0" class="asd_par">
-In this case, the matrix file will be named <tt>myblastfile.b.sym</tt>,
-and the <b>--xo-dat</b> options must be repeated in all runs
-so that the pipeline reconstructs the correct file name(s).</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen</p>
-
-<a name="sealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxdeblast.html">mcxdeblast</a>, <a class="local sibling" href="mclpipeline.html">mclpipeline</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>.</p>
-</body>
-</html>
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-%%EOF
diff --git a/doc/mclcm.1 b/doc/mclcm.1
deleted file mode 100644
index b3fe7ea..0000000
--- a/doc/mclcm.1
+++ /dev/null
@@ -1,337 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mclcm" 1 "16 May 2014" "mclcm 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mclcm \- hierarchical clustering of graphs with mcl
-.SH SYNOPSIS
-
-\fBmclcm\fP <-|fname> [mclcm-options] [-- "mcl options"*]
-
-.di ZV
-.in 0
-.nf \fC
-\fBmclcm\fP <-|fname> -a "-I 4 --shadow=vl"
-\fBmclcm\fP <-|fname> -a "-I 3" -- "-I 5"
-\fBmclcm\fP <-|fname> -a "-I 3" -b1 "" -- "-ph 3 --shadow=vl -I 5"
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBmclcm\fP <-fname>
-\fB[--contract\fP (\fIcontraction mode\fP)\fB]\fP
-\fB[--dispatch\fP (\fIdispatch mode\fP)\fB]\fP
-\fB[--integrate\fP (\fIintegrate mode\fP)\fB]\fP
-\fB[--subcluster\fP (\fIsubcluster mode\fP)\fB]\fP
-\fB[-a\fP <opts> (\fIshared mcl options\fP)\fB]\fP
-\fB[-b1\fP <opts> (\fIdedicated base 1 mcl options\fP)\fB]\fP
-\fB[-b2\fP <opts> (\fIdedicated base 2 mcl options\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-c\fP <fname> (\fIinput clustering\fP)\fB]\fP
-\fB[-n\fP <num> (\fIiteration limit\fP)\fB]\fP
-\fB[--root\fP (\fIensure universe root clustering\fP)\fB]\fP
-\fB[-cone\fP <fname> (\fInested cluster stack file\fP)\fB]\fP
-\fB[-stack\fP <fname> (\fIexpanded cluster stack file\fP)\fB]\fP
-\fB[-coarse\fP <fname> (\fIcoarsened graphs file\fP)\fB]\fP
-\fB[-write\fP (\fIstack,cone,coarse,steps\fP)\fB]\fP
-\fB[-write-base\fP <fname> (\fIwrite base matrix\fP)\fB]\fP
-\fB[-stem\fP <str> (\fIprefix for all outputs\fP)\fB]\fP
-\fB[--mplex=\fPy/n (\fIwrite clusterings separately\fP)\fB]\fP
-\fB[-annot\fP str (\fIdummy annotation option\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-\fB[-q\fP spec (\fIlog levels\fP)\fB]\fP
-\fB[-z\fP (\fIshow default shared options\fP)\fB]\fP
-[-- "mcl options"*]
-.SH DESCRIPTION
-
-The mclcm options may be followed by a number of trailing arguments\&.
-The trailing arguments should be separated from the mclcm options
-by the separator \fC--\fP\&.
-Normally each trailing argument should consist of a set of zero, one, or more mcl arguments
-enclosed in quotes or double quotes to group them together\&.
-These arguments are passed to the successive stages of hierarchical
-clustering\&. They are combined with the default options\&. If an option
-is specified both in the default options list and in a trailing
-options list the latter specification overrides the former\&.
-When the \fB--integrate\fP option is specified the trailing arguments
-must be names of files containing mcl clusterings; see further below\&.
-\fBmclcm\fP has four major modes of operation, namely \fIcontraction\fP (default),
-\fIintegration\fP, \fIdispatch\fP, and \fIsubcluster\fP\&. Each mode is
-described a little below\&. Note though that \fIdispatch\fP mode is not
-the best mode to use for hierarchical clustering\&. It is mostly useful
-to generate multiple mcl clusterings in a single run\&.
-
-In all modes \fBmclcm\fP will generate a file, by default called \fImcl\&.cone\fP\&.
-This is a representation of a hierarchical clustering that is particular
-to mcl\&. It can be converted to \fInewick\fP format like this:
-
-.di ZV
-.in 0
-.nf \fC
- mcxdump -imx-tree mcl\&.cone --newick -o NEWICKFILE
- OR mcxdump -imx-tree mcl\&.cone --newick -o NEWICKFILE -tab TABFILE
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-In the last example, TABFILE should be a file containing a mapping
-from mcl labels to application labels\&. Refer to \fBmcxio(5)\fP for
-more information about tab files and mcl input/ouput formats\&.
-.SH OPTIONS
-
-.ZI 2m "\fB--contract\fP (\fIrepeated contraction mode\fP)"
-\&
-.br
-This is the default mode of operation\&.
-At each successive step of constructing the hierarchy on top of the first
-level mcl clustering, mclcm uses a matrix derived from the input matrix and
-the last computed clustering to compute a contracted graph\&.
-The contracted graph is a graph where the nodes represent the clusters of
-the last clustering\&. The matrix derived from the input graph that is used to
-construct the contracted graph is called the \fIbase matrix\fP\&. The base
-matrix can be either the \fIstart matrix\fP or the \fIexpansion matrix\fP\&.
-The \fIstart matrix\fP is the input matrix after transformations have been
-applied to it (if any)\&.
-The \fIexpansion matrix\fP is the first expanded matrix of some
-mcl process applied to the input graph\&.
-
-By default the base matrix is constructed from either the start matrix
-or the expansion matrix obtained from the first mcl process\&.
-It is possible to use a start matrix derived from special purpose
-mcl transformation parameters (such as \fB-ph\fP and \fB-tf\fP)
-or an expansion matrix derived from a special purpose mcl process\&.
-The \fB-b1\fP and \fB-b2\fP parameters provide the interfaces
-to this functionality\&.
-
-You are advised to start with a high inflation value for the input
-graph and to use shadowing, e\&.g\&. include \fC--shadow=vl\fP in the
-\fB-a\fP argument\&.
-This generally leads to hierarchies that are better balanced\&.
-Shadowing is a transformation where nodes are added to the
-graph, preventing relatively distant nodes from unwanted chaining\&.
-For more information refer to the \fBmcl\fP manual\&.
-The invocations in \fBSYNOPSIS\fP are a good starting point\&.
-.in -2m
-
-.ZI 2m "\fB--dispatch\fP (\fIdifferent mcl processes\fP)"
-\&
-.br
-In this mode each trailing argument is specified as a set of options to pass
-to an mcl process\&. For each trailing argument an mcl process is thus
-computed\&. The set of resulting clusterings is integrated into a hierarchy\&.
-.in -2m
-
-.ZI 2m "\fB--integrate\fP (\fIexisting clusterings\fP)"
-\&
-.br
-This mode is similar to \fIdispatch\fP mode\&. The difference is that with
-this option mclcm simply integrates a set of already existing clusterings\&.
-Each trailing argument must be the name of a file containing a clustering\&.
-The set of clusterings thus specified is integrated into a hierarchy\&.
-.in -2m
-
-.ZI 2m "\fB--subcluster\fP (\fIrepeated sub-clustering\fP)"
-\&
-.br
-In this mode each trailing argument specifies a set of options to pass to an
-mcl process\&. The second clustering process is applied to the graph of
-components induced by the first clustering, resulting in a further
-subdivision of the first clustering\&. This approach is repeated with each
-further trailing argument\&. With this approach, the first clustering will be
-the most coarse clustering\&. Hence, subsequent trailing arguments will
-typically specify increasingly higher inflation values, pre-inflation
-values, and optionally more stringent transformation parameters
-in order to achieve further subdivsions\&.
-.in -2m
-
-.ZI 2m "\fB-a\fP <opts> (\fIshared mcl options\fP)"
-\&
-.br
-Use this to change and/or set the default mcl options for
-all iterations\&. Use quotes if necessary\&.
-Example of usage: -a "-I 5"\&.
-.in -2m
-
-.ZI 2m "\fB-b1\fP <opts> (\fIdedicated base 1 mcl options\fP)"
-\&
-.br
-This will apply the mcl options \fIopts\fP to the input matrix\&. The
-resulting start matrix is used as the base matrix for constructing contracted
-graphs\&.
-.in -2m
-
-.ZI 2m "\fB-b2\fP <opts> (\fIdedicated base 2 mcl options\fP)"
-\&
-.br
-This will apply the mcl options \fIopts\fP to the input matrix and
-compute the first iterand of the corresponding mcl process\&. The first
-iterand, aka the expansion matrix, is used as the base matrix for
-constructing contracted graphs\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-.br
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-c\fP <fname> (\fIinput clustering\fP)"
-\&
-.br
-The hierarchical clustering process will be kicked off by
-the clustering found in \fI<fname>\fP\&.
-.in -2m
-
-.ZI 2m "\fB-n\fP <num> (\fIiteration limit\fP)"
-\&
-.br
-This puts an upper bound to the number of contractions that
-will be performed\&.
-.in -2m
-
-.ZI 2m "\fB--root\fP (\fIensure universe root clustering\fP)"
-\&
-.br
-In case the graph consists of different connected components,
-the last clustering computed by the mclcm process will
-correspond with those connected components\&. This option
-simply adds an artificial clustering where all nodes
-have been joined into a single cluster\&.
-.in -2m
-
-.ZI 2m "\fB-cone\fP <fname> (\fInested cluster stack file\fP)"
-\&
-.br
-File to write the nested cluster stack to\&.
-The nested cluster stack contains a sequence of clusterings,
-each written as an MCL matrix\&.
-The first (bottom) clustering is a clustering of the nodes
-in the input graph\&. Each subsequent clustering is a clustering
-where the nodes are the clusters of the previous clustering\&.
-\fBmcxdump\fP can dump this format if the file name is given as
-the \fB-imx-stack\fP option\&. The explanation
-for the cone/stack discrepancy is simple\&. To mcxdump
-the contents are simply a stack of matrices\&. It does not
-care whether the stack is cone shaped, cylindrical, or
-yet another shape\&.
-.in -2m
-
-.ZI 2m "\fB-stack\fP <fname> (\fIexpanded cluster stack file\fP)"
-\&
-.br
-File to write the expanded cluster stack to\&. The expanded cluster stack is
-similar to the nested cluster stack except that each cluster lists all the
-nodes in the input graph it contains\&.
-\fBmcxdump\fP can dump this format if the file name is given as
-the \fB-imx-stack\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-coarse\fP <fname> (\fIcoarsened graphs file\fP)"
-\&
-.br
-File to write the sequence of coarsened graphs to\&. Each clustering induces a
-coarsened graph where the nodes represent the clusters and an edge between
-two nodes represents the connectivity between the corresponding two
-clusters\&. The computation of this connectivity takes into account all edges
-between the two clusters in in the original graph\&.
-.in -2m
-
-.ZI 2m "\fB-write\fP <tag> (\fIselect output modes\fP)"
-\&
-.br
-Use this option to explicitly specify all of the output types you want
-written in a comma-separated string\&. \fI<tag>\fP may contain
-any of the strings \fIstack\fP, \fIcone\fP, \fIcoarse\fP, \fIsteps\fP\&.
-The current default is to write all of these except \fIcoarse\fP\&.
-The latter dumps the intermediate coarsened (aka contracted) graphs
-to a single file\&.
-.in -2m
-
-.ZI 2m "\fB-write-base\fP <fname> (\fIwrite base matrix\fP)"
-\&
-.br
-Write the base matrix to file\&. This can be useful for debugging
-expectations\&.
-.in -2m
-
-.ZI 2m "\fB-stem\fP <str> (\fIprefix for all outputs\fP)"
-\&
-.br
-All output files share the same prefix\&. The default is \fCmcl\fP
-and can be changed with this option\&.
-.in -2m
-
-.ZI 2m "\fB--mplex\fP=y/n (\fIwrite clusterings separately\fP)"
-\&
-.br
-If turned on each clustering is written in a separate file\&. The first
-clustering is written to the file \fI<stem>\fP\&.3 where \fI<stem>\fP is
-determined by the \fB-stem\fP option\&. For each subsequent clustering
-the index is incremented by two, so clusterings are written to
-files for which the name ends with an odd index\&.
-.in -2m
-
-.ZI 2m "\fB-annot\fP str (\fIdummy annotation option\fP)"
-\&
-.br
-\fBmclcm\fP writes the command line with which it was invoked to the output file
-(either of the \fIcone\fP or \fIstack\fP files)\&. Use this option to include
-any additional information\&. mclcm does nothing with this option except copying
-it as just described\&.
-.in -2m
-
-.ZI 2m "\fB-q\fP spec (\fIlog levels\fP)"
-\&
-.br
-Set the quiet level\&. Read \fBtingea\&.log(7)\fP for syntax and semantics\&.
-.in -2m
-
-.ZI 2m "\fB-z\fP (\fIshow default shared options\fP)"
-\&
-.br
-Show the default mcl options\&. These are used for each mcl invocation as
-successively applied to the input graph and succeeding contracted graphs\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mclcm.html b/doc/mclcm.html
deleted file mode 100644
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-<title>The mclcm manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclcm.ps"><b>mclcm</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclcm — hierarchical clustering of graphs with mcl</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par"><b>mclcm</b> <-|fname> [mclcm-options] [-- "mcl options"*]</p>
-<div class="verbatim"><b>mclcm</b> <-|fname> -a "-I 4 --shadow=vl"
-<b>mclcm</b> <-|fname> -a "-I 3" -- "-I 5"
-<b>mclcm</b> <-|fname> -a "-I 3" -b1 "" -- "-ph 3 --shadow=vl -I 5"</div>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclcm</b> <-fname>
-<a class="intern" href="#opt--contract"><b>[--contract</b> (<i>contraction mode</i>)<b>]</b></a>
-<a class="intern" href="#opt--dispatch"><b>[--dispatch</b> (<i>dispatch mode</i>)<b>]</b></a>
-<a class="intern" href="#opt--integrate"><b>[--integrate</b> (<i>integrate mode</i>)<b>]</b></a>
-<a class="intern" href="#opt--subcluster"><b>[--subcluster</b> (<i>subcluster mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-a"><b>[-a</b> <opts> (<i>shared mcl options</i>)<b>]</b></a>
-<a class="intern" href="#opt-b1"><b>[-b1</b> <opts> (<i>dedicated base 1 mcl options</i>)<b>]</b></a>
-<a class="intern" href="#opt-b2"><b>[-b2</b> <opts> (<i>dedicated base 2 mcl options</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-c"><b>[-c</b> <fname> (<i>input clustering</i>)<b>]</b></a>
-<a class="intern" href="#opt-n"><b>[-n</b> <num> (<i>iteration limit</i>)<b>]</b></a>
-<a class="intern" href="#opt--root"><b>[--root</b> (<i>ensure universe root clustering</i>)<b>]</b></a>
-<a class="intern" href="#opt-cone"><b>[-cone</b> <fname> (<i>nested cluster stack file</i>)<b>]</b></a>
-<a class="intern" href="#opt-stack"><b>[-stack</b> <fname> (<i>expanded cluster stack file</i>)<b>]</b></a>
-<a class="intern" href="#opt-coarse"><b>[-coarse</b> <fname> (<i>coarsened graphs file</i>)<b>]</b></a>
-<a class="intern" href="#opt-write"><b>[-write</b> (<i>stack,cone,coarse,steps</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-base"><b>[-write-base</b> <fname> (<i>write base matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-stem"><b>[-stem</b> <str> (<i>prefix for all outputs</i>)<b>]</b></a>
-<a class="intern" href="#opt--mplex"><b>[--mplex=</b>y/n (<i>write clusterings separately</i>)<b>]</b></a>
-<a class="intern" href="#opt-annot"><b>[-annot</b> str (<i>dummy annotation option</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt-q"><b>[-q</b> spec (<i>log levels</i>)<b>]</b></a>
-<a class="intern" href="#opt-z"><b>[-z</b> (<i>show default shared options</i>)<b>]</b></a>
-[-- "mcl options"*]
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The mclcm options may be followed by a number of trailing arguments.
-The trailing arguments should be separated from the mclcm options
-by the separator <tt>--</tt>.
-Normally each trailing argument should consist of a set of zero, one, or more mcl arguments
-enclosed in quotes or double quotes to group them together.
-These arguments are passed to the successive stages of hierarchical
-clustering. They are combined with the default options. If an option
-is specified both in the default options list and in a trailing
-options list the latter specification overrides the former.
-When the <b>--integrate</b> option is specified the trailing arguments
-must be names of files containing mcl clusterings; see further below.
-<b>mclcm</b> has four major modes of operation, namely <i>contraction</i> (default),
-<i>integration</i>, <i>dispatch</i>, and <i>subcluster</i>. Each mode is
-described a little below. Note though that <i>dispatch</i> mode is not
-the best mode to use for hierarchical clustering. It is mostly useful
-to generate multiple mcl clusterings in a single run.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-In all modes <b>mclcm</b> will generate a file, by default called <i>mcl.cone</i>.
-This is a representation of a hierarchical clustering that is particular
-to mcl. It can be converted to <i>newick</i> format like this:
-</p>
-<div class="verbatim"> mcxdump -imx-tree mcl.cone --newick -o NEWICKFILE
- OR mcxdump -imx-tree mcl.cone --newick -o NEWICKFILE -tab TABFILE</div>
-<p style="margin-bottom:0" class="asd_par">
-In the last example, TABFILE should be a file containing a mapping
-from mcl labels to application labels. Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for
-more information about tab files and mcl input/ouput formats.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--contract"></a><b>--contract</b> (<i>repeated contraction mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This is the default mode of operation.
-At each successive step of constructing the hierarchy on top of the first
-level mcl clustering, mclcm uses a matrix derived from the input matrix and
-the last computed clustering to compute a contracted graph.
-The contracted graph is a graph where the nodes represent the clusters of
-the last clustering. The matrix derived from the input graph that is used to
-construct the contracted graph is called the <i>base matrix</i>. The base
-matrix can be either the <i>start matrix</i> or the <i>expansion matrix</i>.
-The <i>start matrix</i> is the input matrix after transformations have been
-applied to it (if any).
-The <i>expansion matrix</i> is the first expanded matrix of some
-mcl process applied to the input graph.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-By default the base matrix is constructed from either the start matrix
-or the expansion matrix obtained from the first mcl process.
-It is possible to use a start matrix derived from special purpose
-mcl transformation parameters (such as <b>-ph</b> and <b>-tf</b>)
-or an expansion matrix derived from a special purpose mcl process.
-The <b>-b1</b> and <b>-b2</b> parameters provide the interfaces
-to this functionality.</p>
-<p style="margin-bottom:0" class="asd_par">
-You are advised to start with a high inflation value for the input
-graph and to use shadowing, e.g. include <tt>--shadow=vl</tt> in the
-<b>-a</b> argument.
-This generally leads to hierarchies that are better balanced.
-Shadowing is a transformation where nodes are added to the
-graph, preventing relatively distant nodes from unwanted chaining.
-For more information refer to the <b>mcl</b> manual.
-The invocations in <a class="intern" href="#synopsis">SYNOPSIS</a> are a good starting point.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--dispatch"></a><b>--dispatch</b> (<i>different mcl processes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-In this mode each trailing argument is specified as a set of options to pass
-to an mcl process. For each trailing argument an mcl process is thus
-computed. The set of resulting clusterings is integrated into a hierarchy.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--integrate"></a><b>--integrate</b> (<i>existing clusterings</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This mode is similar to <i>dispatch</i> mode. The difference is that with
-this option mclcm simply integrates a set of already existing clusterings.
-Each trailing argument must be the name of a file containing a clustering.
-The set of clusterings thus specified is integrated into a hierarchy.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--subcluster"></a><b>--subcluster</b> (<i>repeated sub-clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-In this mode each trailing argument specifies a set of options to pass to an
-mcl process. The second clustering process is applied to the graph of
-components induced by the first clustering, resulting in a further
-subdivision of the first clustering. This approach is repeated with each
-further trailing argument. With this approach, the first clustering will be
-the most coarse clustering. Hence, subsequent trailing arguments will
-typically specify increasingly higher inflation values, pre-inflation
-values, and optionally more stringent transformation parameters
-in order to achieve further subdivsions.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-a"></a><b>-a</b> <opts> (<i>shared mcl options</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this to change and/or set the default mcl options for
-all iterations. Use quotes if necessary.
-Example of usage: -a "-I 5".</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-b1"></a><b>-b1</b> <opts> (<i>dedicated base 1 mcl options</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This will apply the mcl options <i>opts</i> to the input matrix. The
-resulting start matrix is used as the base matrix for constructing contracted
-graphs.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-b2"></a><b>-b2</b> <opts> (<i>dedicated base 2 mcl options</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This will apply the mcl options <i>opts</i> to the input matrix and
-compute the first iterand of the corresponding mcl process. The first
-iterand, aka the expansion matrix, is used as the base matrix for
-constructing contracted graphs.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-c"></a><b>-c</b> <fname> (<i>input clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The hierarchical clustering process will be kicked off by
-the clustering found in <i><fname></i>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-n"></a><b>-n</b> <num> (<i>iteration limit</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This puts an upper bound to the number of contractions that
-will be performed.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--root"></a><b>--root</b> (<i>ensure universe root clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-In case the graph consists of different connected components,
-the last clustering computed by the mclcm process will
-correspond with those connected components. This option
-simply adds an artificial clustering where all nodes
-have been joined into a single cluster.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cone"></a><b>-cone</b> <fname> (<i>nested cluster stack file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-File to write the nested cluster stack to.
-The nested cluster stack contains a sequence of clusterings,
-each written as an MCL matrix.
-The first (bottom) clustering is a clustering of the nodes
-in the input graph. Each subsequent clustering is a clustering
-where the nodes are the clusters of the previous clustering.
-<b>mcxdump</b> can dump this format if the file name is given as
-the <b>-imx-stack</b> option. The explanation
-for the cone/stack discrepancy is simple. To mcxdump
-the contents are simply a stack of matrices. It does not
-care whether the stack is cone shaped, cylindrical, or
-yet another shape.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-stack"></a><b>-stack</b> <fname> (<i>expanded cluster stack file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-File to write the expanded cluster stack to. The expanded cluster stack is
-similar to the nested cluster stack except that each cluster lists all the
-nodes in the input graph it contains.
-<b>mcxdump</b> can dump this format if the file name is given as
-the <b>-imx-stack</b> option.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-coarse"></a><b>-coarse</b> <fname> (<i>coarsened graphs file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-File to write the sequence of coarsened graphs to. Each clustering induces a
-coarsened graph where the nodes represent the clusters and an edge between
-two nodes represents the connectivity between the corresponding two
-clusters. The computation of this connectivity takes into account all edges
-between the two clusters in in the original graph.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write"></a><b>-write</b> <tag> (<i>select output modes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this option to explicitly specify all of the output types you want
-written in a comma-separated string. <i><tag></i> may contain
-any of the strings <i>stack</i>, <i>cone</i>, <i>coarse</i>, <i>steps</i>.
-The current default is to write all of these except <i>coarse</i>.
-The latter dumps the intermediate coarsened (aka contracted) graphs
-to a single file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-base"></a><b>-write-base</b> <fname> (<i>write base matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the base matrix to file. This can be useful for debugging
-expectations.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-stem"></a><b>-stem</b> <str> (<i>prefix for all outputs</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-All output files share the same prefix. The default is <tt>mcl</tt>
-and can be changed with this option.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mplex"></a><b>--mplex</b>=y/n (<i>write clusterings separately</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If turned on each clustering is written in a separate file. The first
-clustering is written to the file <i><stem></i>.3 where <i><stem></i> is
-determined by the <b>-stem</b> option. For each subsequent clustering
-the index is incremented by two, so clusterings are written to
-files for which the name ends with an odd index.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-annot"></a><b>-annot</b> str (<i>dummy annotation option</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mclcm</b> writes the command line with which it was invoked to the output file
-(either of the <i>cone</i> or <i>stack</i> files). Use this option to include
-any additional information. mclcm does nothing with this option except copying
-it as just described.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-q"></a><b>-q</b> spec (<i>log levels</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the quiet level. Read <a class="local sibling" href="tingea.log.html">tingea.log</a> for syntax and semantics.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-z"></a><b>-z</b> (<i>show default shared options</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Show the default mcl options. These are used for each mcl invocation as
-successively applied to the input graph and succeeding contracted graphs.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
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diff --git a/doc/mclcm.ps b/doc/mclcm.ps
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-<title>The MCL family</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclfamily.ps"><b>mcl</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclfamily — a description of the mcl family of cluster applications.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> is an implementation of the Markov Cluster Algorithm, aka MCL algoritm.
-It is described in the <a class="local sibling" href="mcl.html">mcl manual</a>.
-Several other applications are part of the MCL distribution. This manual pages
-gives an overview.</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcl.html">mcl</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">the cluster algorithm</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclfaq.html">mclfaq</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">MCL Frequently Asked Questions</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxio.html">mcxio</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">the network/matrix input/output format</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcx.html">mcx</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">general network/matrix tasks</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdiameter.html">mcx diameter</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute diameter of an undirected network</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxctty.html">mcx ctty</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute betweenness centrality</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxclcf.html">mcx clcf</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute clustering coefficient</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxerdos.html">mcx erdos</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute shortest paths in graphs</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxquery.html">mcx query</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">analyse networks at different thresholds</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxalter.html">mcx alter</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">apply network transformations</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxconvert.html">mcx convert</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">convert between interchange/binary storage types</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxarray.html">mcxarray</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">transform array data to MCL matrices</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdump.html">mcxdump</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">dump a matrix optionally with label substitions</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxload.html">mcxload</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">load label data into matrix and tab files</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxrand.html">mcxrand</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">randomly remove, add, and perturb edge weights</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxmap.html">mcxmap</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">relabel indices in a graph/matrix</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxsubs.html">mcxsubs</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">extracting submatrices in various ways</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxi.html">mcxi</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">general matrix operations</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxassemble.html">mcxassemble</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">create matrices from raw data</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clm.html">clm</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">general graph-clustering related tasks</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmdist.html">clm dist</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute split/join distance between clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmvol.html">clm vol</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">derive node volatility scores from a set of clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clminfo.html">clm info</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute performance measure for clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmmeet.html">clm meet</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">compute intersection of clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmmate.html">clm mate</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">find best matching clusters between clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmclose.html">clm close</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">fetch connected components from graphs or subgraphs</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmimac.html">clm imac</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">interpret MCL iterand/matrix as clustering</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmorder.html">clm order</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">reorder indices to represent blocks from different clusterings</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmresidue.html">clm residue</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">extend subgraph clustering</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmformat.html">clmformat</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">display clusters as html or txt files</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclpipeline.html">mclpipeline</a></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">parsing/assembly/clustering/display</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclblastline.html">mclblastline</a> <tt>*</tt></div></div>
-<div class=" item_text " style="margin-left:15em">
-<p style="margin-top:0em; margin-bottom:0em">BLAST pipeline</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> <tt>*</tt></div></div>
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-<title>The MCL FAQ</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclfaq.ps"><b>MCL FAQ</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#resources">RESOURCES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#toc">TOC</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#faq">FAQ</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#bugs">BUGS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#notes">NOTES</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclfaq — faqs and facts about the MCL cluster algorithm.</p>
-<p style="margin-bottom:0" class="asd_par">
-MCL refers to the generic MCL algorithm and the MCL process on which the
-algorithm is based. <b>mcl</b> refers to the implementation. This FAQ answers
-questions related to both. In some places MCL is written where MCL or mcl
-can be read. This is the case for example in
-<a class="intern" href="#kind">section 3, What kind of graphs</a>.
-It should in general be obvious from the context.</p>
-<p style="margin-bottom:0" class="asd_par">
-This FAQ does not begin to attempt to explain the motivation
-and mathematics behind the MCL algorithm - the internals are not
-explained. A broad view is given in faq <a class="intern" href="#overview">1.2</a>,
-and see also faq <a class="intern" href="#innards">1.5</a> and section <a class="intern" href="#references">REFERENCES</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Some additional sections preceed the actual faq entries.
-The TOC section contains a listing of all questions.
-<b>Clicking on the number of a question</b>
-(where it is answered) will take you to
-the corresponding section of the table of contents.
-</p>
-
-<a name="resources"></a>
-<h2>RESOURCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-The manual pages for all the utilities that come with <b>mcl</b>;
-refer to <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview.</p>
-<p style="margin-bottom:0" class="asd_par">
-See the <a class="intern" href="#references">REFERENCES</a> Section for publications detailing the
-mathematics behind the MCL algorithm.</p>
-
-<a name="toc"></a>
-<h2>TOC</h2>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-general"></a><a class="quiet" href="#general"><b>1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#general"><b>General questions</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.1"></a> <a class="intern" href="#faq1.1"><b>1.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.1"><b>For whom is mcl and for whom is this FAQ?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-overview"></a> <a class="intern" href="#overview"><b>1.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#overview"><b>What is the relationship between the MCL process, the MCL algorithm, and the 'mcl' implementation?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.3"></a> <a class="intern" href="#faq1.3"><b>1.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.3"><b>What do the letters MCL stand for?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.4"></a> <a class="intern" href="#faq1.4"><b>1.4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.4"><b>How could you be so feebleminded to use MCL as abbreviation? Why
-is it labeled 'Markov cluster' anyway?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-innards"></a> <a class="intern" href="#innards"><b>1.5</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#innards"><b>Where can I learn about the innards of the MCL algorithm/process?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq1.6"></a> <a class="intern" href="#faq1.6"><b>1.6</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq1.6"><b>For which platforms is mcl available?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-versioning"></a> <a class="intern" href="#versioning"><b>1.7</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#versioning"><b>How does mcl's versioning scheme work?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-ioformat"></a><a class="quiet" href="#ioformat"><b>2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#ioformat"><b>Input format</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq2.1"></a> <a class="intern" href="#faq2.1"><b>2.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq2.1"><b>How can I get my data into the MCL matrix format?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-kind"></a><a class="quiet" href="#kind"><b>3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#kind"><b>What kind of graphs</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.1"></a> <a class="intern" href="#faq3.1"><b>3.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.1"><b>What is legal input for MCL?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.2"></a> <a class="intern" href="#faq3.2"><b>3.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.2"><b>What is sensible input for MCL?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.3"></a> <a class="intern" href="#faq3.3"><b>3.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.3"><b>Does MCL work for weighted graphs?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.4"></a> <a class="intern" href="#faq3.4"><b>3.4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.4"><b>Does MCL work for directed graphs?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.5"></a> <a class="intern" href="#faq3.5"><b>3.5</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.5"><b>Can MCL work for lattices / directed acyclic graphs / DAGs?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.6"></a> <a class="intern" href="#faq3.6"><b>3.6</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.6"><b>Does MCL work for tree graphs?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-whatkind"></a> <a class="intern" href="#whatkind"><b>3.7</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#whatkind"><b>For what kind of graphs does MCL work well and for which does it not?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-goodinput"></a> <a class="intern" href="#goodinput"><b>3.8</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#goodinput"><b>What makes a good input graph?
-How do I construct the similarities?
-How to make them satisfy this Markov condition?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-directedinput"></a> <a class="intern" href="#directedinput"><b>3.9</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#directedinput"><b>My input graph is directed. Is that bad?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq3.10"></a> <a class="intern" href="#faq3.10"><b>3.10</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq3.10"><b>Why does mcl like undirected graphs and why does it
-dislike uni-directed graphs so much?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-checksymmetry"></a> <a class="intern" href="#checksymmetry"><b>3.11</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#checksymmetry"><b>How do I check that my graph/matrix is symmetric/undirected?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-speed"></a><a class="quiet" href="#speed"><b>4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#speed"><b>Speed and complexity</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-howfast"></a> <a class="intern" href="#howfast"><b>4.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#howfast"><b>How fast is mcl/MCL?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-stats"></a> <a class="intern" href="#stats"><b>4.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#stats"><b>What statistics are available?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-colsort"></a> <a class="intern" href="#colsort"><b>4.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#colsort"><b>Does this implementation need to sort vectors?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-approx"></a> <a class="intern" href="#approx"><b>4.4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#approx"><b>mcl does not compute the ideal MCL process!</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-comparison"></a><a class="quiet" href="#comparison"><b>5</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#comparison"><b>Comparison with other algorithms</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-xyzbetter"></a> <a class="intern" href="#xyzbetter"><b>5.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#xyzbetter"><b>I've read someplace that XYZ is much better than MCL</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-xyzslower"></a> <a class="intern" href="#xyzslower"><b>5.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#xyzslower"><b>I've read someplace that MCL is slow [compared with XYZ]</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-resource"></a><a class="quiet" href="#resource"><b>6</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#resource"><b>Resource tuning / accuracy</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-wdymbrt"></a> <a class="intern" href="#wdymbrt"><b>6.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#wdymbrt"><b>What do you mean by resource tuning?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq6.2"></a> <a class="intern" href="#faq6.2"><b>6.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq6.2"><b>How do I compute the maximum amount of RAM needed by mcl?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-pcmp"></a> <a class="intern" href="#pcmp"><b>6.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#pcmp"><b>How much does the mcl clustering differ from the clustering resulting
-from a perfectly computed MCL process?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-enoughresources"></a> <a class="intern" href="#enoughresources"><b>6.4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#enoughresources"><b>How do I know that I am using enough resources?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-nmap"></a> <a class="intern" href="#nmap"><b>6.5</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#nmap"><b>Where is the mathematical analysis of this mcl pruning strategy?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-qsep"></a> <a class="intern" href="#qsep"><b>6.6</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#qsep"><b>What qualitative statements can be made about the effect of pruning?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq6.7"></a> <a class="intern" href="#faq6.7"><b>6.7</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq6.7"><b>At different high resource levels my clusterings are not identical.
-How can I trust the output clustering?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-granularity"></a><a class="quiet" href="#granularity"><b>7</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#granularity"><b>Tuning cluster granularity</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq7.1"></a> <a class="intern" href="#faq7.1"><b>7.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq7.1"><b>How do I tune cluster granularity?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq7.2"></a> <a class="intern" href="#faq7.2"><b>7.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq7.2"><b>The effect of inflation on cluster granularity.</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-degree_granul"></a> <a class="intern" href="#degree_granul"><b>7.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#degree_granul"><b>The effect of node degrees on cluster granularity.</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-simil_granul"></a> <a class="intern" href="#simil_granul"><b>7.4</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#simil_granul"><b>The effect of edge weight differentiation on cluster granularity.</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-implement"></a><a class="quiet" href="#implement"><b>8</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#implement"><b>Implementing the MCL algorithm</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-faq8.1"></a> <a class="intern" href="#faq8.1"><b>8.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#faq8.1"><b>How easy is it to implement the MCL algorithm?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-overlap"></a><a class="quiet" href="#overlap"><b>9</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#overlap"><b>Cluster overlap / MCL iterand cluster interpretation</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-olapintro"></a> <a class="intern" href="#olapintro"><b>9.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#olapintro"><b>Introduction</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-ccco"></a> <a class="intern" href="#ccco"><b>9.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#ccco"><b>Can the clusterings returned by mcl contain overlap?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-imac"></a> <a class="intern" href="#imac"><b>9.3</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#imac"><b>How do I obtain the clusterings associated with MCL iterands?</b></a>
-</div>
-</div>
-<hr>
-<div class=" itemize " style="margin-top:0em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="toc-misc"></a><a class="quiet" href="#misc"><b>10</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="quiet" href="#misc"><b>Miscellaneous</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-defaults"></a> <a class="intern" href="#defaults"><b>10.1</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#defaults"><b>How do I find the default settings of mcl?</b></a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-1em"><a name="toc-next"></a> <a class="intern" href="#next"><b>10.2</b></a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<a class="intern" href="#next"><b>What's next?</b></a>
-</div>
-</div>
-<br><br>
-
-<a name="faq"></a>
-<h2>FAQ</h2>
-
-<div align=center>
-<h3><a name="general"></a><a class="quiet" href="#toc-general">1</a><br>General questions
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.1"></a> <a class="quiet" href="#toc-general">1.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For whom is mcl and for whom is this FAQ?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For everybody with an appetite for graph clustering.
-Regarding the FAQ, I have kept the amount of
-mathematics as low as possible, as far as matrix analysis is concerned.
-Inevitably, some terminology pops up and some references are made to the
-innards of the MCL algorithm, especially in the section on resources and
-accuracy. Graph terminology is used somewhat more carelessly though. The
-future might bring definition entries, right now you have to do without.
-Mathematically inclined people may be interested in the pointers found in
-the <a class="intern" href="#references">REFERENCES</a> section.</p>
-<p style="margin-bottom:0" class="asd_par">
-Given this mention of mathematics, let me point out this one time only that
-using <b>mcl</b> is extremely straightforward anyway. You need only mcl and an
-input graph (refer to the <a class="local sibling" href="mcl.html">mcl manual page</a>), and many people
-trained in something else than mathematics are using mcl happily.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="overview"></a> <a class="quiet" href="#toc-general">1.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What is the relationship between the MCL process, the MCL algorithm, and the 'mcl' implementation?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mcl</b> is what you use for clustering. It implements the MCL algorithm,
-which is a cluster algorithm for graphs. The MCL algorithm is basically
-a shell in which the MCL process is computed and interpreted. I will
-describe them in the natural, reverse, order.</p>
-<p style="margin-bottom:0" class="asd_par">
-The MCL process generates a sequence of stochastic matrices given some initial
-stochastic matrix. The elements with even index are obtained by
-<i>expanding</i> the previous element, and the elements with odd index are
-obtained by <i>inflating</i> the previous element given some inflation
-constant. Expansion is nothing but normal matrix squaring, and inflation is
-a particular way of rescaling the entries of a stochastic matrix such that
-it remains stochastic.</p>
-<p style="margin-bottom:0" class="asd_par">
-The sequence of MCL elements (from the MCL process) is in principle without end,
-but what happens is that the elements converge to some specific kind of
-matrix, called the <i>limit</i> of the process. The heuristic underlying MCL
-predicts that the interaction of expansion with inflation will lead to a
-limit exhibiting cluster structure in the graph associated with the
-initial matrix. This is indeed the case, and several mathematical results
-tie MCL iterands and limits and the MCL interpretation together
-(<a class="intern" href="#references">REFERENCES</a>).</p>
-<p style="margin-bottom:0" class="asd_par">
-The MCL algorithm is simply a shell around the MCL process. It
-transforms an input graph into an initial matrix suitable for
-starting the process. It sets inflation parameters and stops the
-MCL process once a limit is reached, i.e. convergence is detected.
-The result is then interpreted as a clustering.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>mcl</b> implementation supplies the functionality of the MCL algorithm,
-with some extra facilities for manipulation of the input graph, interpreting
-the result, manipulating resources while computing the process, and
-monitoring the state of these manipulations.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.3"></a> <a class="quiet" href="#toc-general">1.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What do the letters MCL stand for?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For <i>Markov Cluster</i>. The MCL algorithm is a <b>cluster</b> algorithm
-that is basically a shell in which an algebraic process is computed.
-This process iteratively generates stochastic matrices, also known
-as <b>Markov</b> matrices, named after the famous Russian
-mathematician Andrei Markov.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.4"></a> <a class="quiet" href="#toc-general">1.4</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How could you be so feebleminded to use MCL as abbreviation? Why
-is it labeled 'Markov cluster' anyway?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Sigh. It is a widely known fact that a TLA or Three-Letter-Acronym
-is <i>the canonical self-describing abbreviation for the name
-of a species with which computing terminology is infested</i> (quoted
-from the Free Online Dictionary of Computing). Back when I was
-thinking of a nice tag for this cute algorithm, I was
-totally unaware of this. I naturally dismissed <i>MC</i>
-(and would still do that today). Then <i>MCL</i> occurred
-to me, and without giving it much thought I started using it.
-A Google search (or was I still using Alta-Vista back then?)
-might have kept me from going astray.</p>
-<p style="margin-bottom:0" class="asd_par">
-Indeed, <i>MCL</i> is used as a tag for <i>Macintosh Common Lisp</i>,
-<i>Mission Critical Linux</i>, <i>Monte Carlo Localization</i>, <i>MUD Client
-for Linux</i>, <i>Movement for Canadian Literacy</i>, and a gazillion other
-things — refer to the file <a class="extern" href="mclmcl.txt">mclmcl.txt</a>. Confusing. It seems that
-the three characters <tt>MCL</tt> possess otherworldly magical powers making
-them an ever so strange and strong attractor in the space of TLAs. It
-probably helps that Em-See-Ell (Em-Say-Ell in Dutch) has some rhythm
-to it as well. Anyway MCL stuck, and it's here to stay.</p>
-<p style="margin-bottom:0" class="asd_par">
-On a more general level, the label <i>Markov Cluster</i> is not an entirely
-fortunate choice either. Although phrased in the language of stochastic
-matrices, MCL theory bears very little relation to Markov theory, and is
-much closer to matrix analysis (including Hilbert's distance) and the theory
-of dynamical systems. No results have been derived in the latter framework,
-but many conjectures are naturally posed in the language of dynamical
-systems.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="innards"></a> <a class="quiet" href="#toc-general">1.5</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Where can I learn about the innards of the MCL algorithm/process?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Currently, the most basic explanation of the MCL algorithm is found in the
-technical report <a class="intern" href="#cafg">[2]</a>. It contains sections on several other
-(related) subjects though, and it assumes some working knowledge on graphs,
-matrix arithmetic, and stochastic matrices.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq1.6"></a> <a class="quiet" href="#toc-general">1.6</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For which platforms is mcl available?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-It should compile and run on virtually any flavour of UNIX (including Linux
-and the BSD variants of course). Following the instructions in the INSTALL
-file shipped with mcl should be straightforward and sufficient. Courtesy to
-Joost van Baal who completely autofooled <b>mcl</b>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Building MCL on Wintel (Windows on Intel chip) should be straightforward if
-you use the full suite of cygwin tools. Install cygwin if you do not have it
-yet. In the cygwin shell, unpack mcl and simply issue the commands
-<i>./configure, make, make install</i>, i.e. follow the instructions in
-INSTALL.</p>
-<p style="margin-bottom:0" class="asd_par">
-This MCL implementation should also build successfully on Mac OS X.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="versioning"></a> <a class="quiet" href="#toc-general">1.7</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How does mcl's versioning scheme work?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-The current setup, which I hope to continue, is this. All releases are
-identified by a date stamp. For example 02-095 denotes day 95 in the year
-2002. This date stamp agrees (as of April 2000) with the (differently
-presented) date stamp used in all manual pages shipped with that release.
-For example, the date stamp of the FAQ you are reading is <b>16 May 2014</b>,
-which corresponds with the MCL stamp <b>14-137</b>.
-The Changelog file contains a list of what's changed/added with each
-release. Currently, the date stamp is the primary way of identifying an <b>mcl</b>
-release. When asked for its version by using <b>--version</b>, mcl
-outputs both the date stamp and a version tag (see below).</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="ioformat"></a><a class="quiet" href="#toc-ioformat">2</a><br>Input format
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq2.1"></a> <a class="quiet" href="#toc-ioformat">2.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How can I get my data into the MCL matrix format?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-This is described in the <a class="local" href="clmprotocols.html">protocols manual page</a>.
-</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="kind"></a><a class="quiet" href="#toc-kind">3</a><br>What kind of graphs
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.1"></a> <a class="quiet" href="#toc-kind">3.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What is legal input for MCL?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Any graph (encoded as a matrix of similarities) that is nonnegative,
-i.e. all similarities are greater than or equal to zero.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.2"></a> <a class="quiet" href="#toc-kind">3.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What is sensible input for MCL?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Graphs can be weighted, and they should preferably be symmetric. Weights
-should carry the meaning of similarity, <i>not</i> distance. These weights or
-similarities are incorporated into the MCL algorithm in a meaningful way.
-Graphs should certainly not contain parts that are (almost) cyclic, although
-nothing stops you from experimenting with such input.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.3"></a> <a class="quiet" href="#toc-kind">3.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Does MCL work for weighted graphs?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Yes, unequivocally. They should preferably be symmetric/undirected though.
-See entries <a class="intern" href="#whatkind">3.7</a> and <a class="intern" href="#goodinput">3.8</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.4"></a> <a class="quiet" href="#toc-kind">3.4</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Does MCL work for directed graphs?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Maybe, with a big caveat. See entries <a class="intern" href="#goodinput">3.8</a>
-and <a class="intern" href="#directedinput">3.9</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.5"></a> <a class="quiet" href="#toc-kind">3.5</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Can MCL work for lattices / directed acyclic graphs / DAGs?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Such graphs [term] can surely exhibit clear cluster structure. If they
-do, there is only one way for mcl to find out. You have to change all arcs
-to edges, i.e. if there is an arc from i to j with similarity s(i,j) — by
-the DAG property this implies s(j,i) = 0 — then make s(j,i) equal to s(i,j).</p>
-<p style="margin-bottom:0" class="asd_par">
-This may feel like throwing away valuable information, but in truth the
-information that is thrown away (direction) is <i>not</i> informative with
-respect to the presence of cluster structure. This may well deserve a longer
-discussion than would be justified here.</p>
-<p style="margin-bottom:0" class="asd_par">
-If your graph is directed and acyclic (or parts of it are), you can
-transform it before clustering with mcl by using <b>-tf</b> <b>'#max()'</b>, e.g.
-</p>
-<div class="verbatim"> mcl YOUR-GRAPH -I 3.0 -tf '#max()'</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.6"></a> <a class="quiet" href="#toc-kind">3.6</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Does MCL work for tree graphs?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Nah, I don't think so. More info at entry <a class="intern" href="#whatkind">3.7</a>.
-You could consider the <a target="_parent" class="extern" href="http://en.wikipedia.org/wiki/Strahler_number">Strahler number</a>,
-which is numerical measure of branching complexity.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="whatkind"></a> <a class="quiet" href="#toc-kind">3.7</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>For what kind of graphs does MCL work well and for which does it not?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Graphs in which the diameter [term] of (subgraphs induced by) natural
-clusters is not too large. Additionally, graphs should preferably be
-(almost) undirected (see entry below) and not so sparse that the cardinality
-of the edge set is close to the number of nodes.</p>
-<p style="margin-bottom:0" class="asd_par">
-A class of such very sparse graphs is that of tree graphs. You might look
-into <i>graph visualization</i> software and research if you are interested
-in decomposing trees into 'tight' subtrees.</p>
-<p style="margin-bottom:0" class="asd_par">
-The diameter criterion could be violated by
-neighbourhood graphs derived from vector data. In the specific case
-of 2 and 3 dimensional data, you might be interested
-in <i>image segmentation</i> and <i>boundary detection</i>, and for
-the general case there is a host of other algorithms out there. [add]</p>
-<p style="margin-bottom:0" class="asd_par">
-In case of weighted graphs, the notion of <i>diameter</i> is sometimes not
-applicable. Generalizing this notion requires inspecting the <i>mixing
-properties</i> of a subgraph induced by a natural cluster in terms of its
-spectrum. However, the diameter statement is something grounded on heuristic
-considerations (confirmed by practical evidence <a class="intern" href="#pcfgcmce">[4]</a>)
-to begin with, so you should probably forget about mixing properties.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="goodinput"></a> <a class="quiet" href="#toc-kind">3.8</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What makes a good input graph?
-How do I construct the similarities?
-How to make them satisfy this Markov condition?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-To begin with the last one: you <i>need not and must not</i> make the
-input graph such that it is stochastic aka Markovian [term]. What you
-need to do is make a graph that is preferably symmetric/undirected,
-i.e. where s(i,j) = s(j,i) for all nodes i and j. It need not be
-perfectly undirected, see the following faq for a discussion of that.
-<b>mcl</b> will work with the graph of random walks that is associated
-with your input graph, and that is the natural state of affairs.</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph should preferably be honest in the sense that if <tt>s(x,y)=N</tt>
-and <tt>s(x,z)=200N</tt> (i.e. the similarities differ by a factor 200), then
-this should really reflect that the similarity of <tt>y</tt> to <tt>x</tt> is neglectible
-compared with the similarity of <tt>z</tt> to <tt>x</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-For the rest, anything goes. Try to get a feeling by experimenting.
-Sometimes it is a good idea to filter out high-frequency
-and/or low-frequency data, i.e. nodes with either very many neighbours
-or extremely few neighbours.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="directedinput"></a> <a class="quiet" href="#toc-kind">3.9</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>My input graph is directed. Is that bad?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-It depends. The class of directed graphs can be viewed as a spectrum going
-from undirected graphs to uni-directed graphs. <i>Uni-directed</i> is
-terminology I am inventing here, which I define as the property that
-for all node pairs i, j, at least one of s(i,j) or s(j,i) is zero. In other
-words, if there is an arc going from i to j in a uni-directed graph, then
-there is no arc going from j to i. I call a node pair i, j,
-<i>almost uni-directed</i> if s(i,j) << s(j,i) or vice versa,
-i.e. if the similarities differ by an order of magnitude.</p>
-<p style="margin-bottom:0" class="asd_par">
-If a graph does not have (large) subparts that are (almost) uni-directed,
-have a go with mcl. Otherwise, try to make your graph less uni-directed.
-You are in charge, so do anything with your graph as you see fit,
-but preferably abstain from feeding mcl uni-directed graphs.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq3.10"></a> <a class="quiet" href="#toc-kind">3.10</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Why does mcl like undirected graphs and why does it
-dislike uni-directed graphs so much?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Mathematically, the mcl iterands will be <i>nice</i> when the input graph is
-symmetric, where <i>nice</i> is in this case <i>diagonally symmetric to a
-semi-positive definite matrix</i> (ignore as needed). For one thing, such nice
-matrices can be interpreted as clusterings in a way that generalizes the
-interpretation of the mcl limit as a clustering (if you are curious to these
-intermediate clusterings, see <a class="intern" href="#imac">faq entry 9.3</a>).
-See the <a class="intern" href="#references">REFERENCES</a> section for pointers to mathematical
-publications.</p>
-<p style="margin-bottom:0" class="asd_par">
-The reason that mcl dislikes uni-directed graphs is not very mcl specific,
-it has more to do with the clustering problem itself.
-Somehow, directionality thwarts the notion of cluster structure.
-[add].</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="checksymmetry"></a> <a class="quiet" href="#toc-kind">3.11</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I check that my graph/matrix is symmetric/undirected?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Whether your graph is created by third-party software or by custom sofware
-written by someone you know (e.g. yourself), it is advisable to test whether
-the software generates symmetric matrices. This can be done as follows
-using the <a class="local sibling" href="mcxi.html">mcxi utility</a>, assuming that you want to test the
-matrix stored in file <tt>matrix.mci</tt>. The mcxi utility should be available
-on your system if mcl was installed in the normal way.</p>
-<div class="verbatim">mcxi /matrix.mci lm tp -1 mul add /check wm</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This loads the graph/matrix stored in <tt>matrix.mci</tt> into <b>mcxi</b>'s memory with
-the <b>mcxi</b> <i>lm</i> primitive. — the leading slash is how strings are
-introduced in the stack language interpreted by <b>mcxi</b>. The transpose of
-that matrix is then pushed on the stack with the <i>tp</i> primitive and
-multiplied by minus one. The two matrices are added, and the result is
-written to the file <tt>check</tt>.
-The transposed matrix is the mirrored version of the original matrix stored
-in <tt>matrix.mci</tt>. If a graph/matrix is undirected/symmetric, the mirrored
-image is necessarily the same, so if you subtract one from the other it
-should yield an all zero matrix.</p>
-<p style="margin-bottom:0" class="asd_par">
-Thus, the file <tt>check</tt> <i>should look like this</i>:</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions <num>x<num>
-)
-(mclmatrix
-begin
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Where <tt><num></tt> is the same as in the file <tt>matrix.mci</tt>. If this is not
-the case, find out what's prohibiting you from feeding mcl symmetric
-matrices. Note that any nonzero entries found in the matrix stored as
-<tt>check</tt> correspond to node pairs for which the arcs in the two possible
-directions have different weight.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="speed"></a><a class="quiet" href="#toc-speed">4</a><br>Speed and complexity
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="howfast"></a> <a class="quiet" href="#toc-speed">4.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How fast is mcl/MCL?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-It's fast - here is how and why. Let <tt>N</tt> be the number of nodes in the input
-graph. A straigtforward implementation of MCL will have time and space
-complexity respecively <tt>O(N^3)</tt> (i.e. cubic in <tt>N</tt>) and <tt>O(N^2)</tt>
-(quadratic in <tt>N</tt>). So you don't want one of those.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcl</b> implements a slightly perturbed version of the MCL process,
-as discussed in section <a class="intern" href="#resource">Resource tuning / accuracy</a>.
-Refer to that section for a more extensive discussion of all
-the aspects involved. This section is only concerned with the high-level
-view of things <i>and</i> the nitty gritty complexity details.</p>
-<p style="margin-bottom:0" class="asd_par">
-While computing the square of a matrix
-(the product of that matrix with itself), mcl keeps the matrix sparse
-by allowing a certain maximum number of nonzero entries
-per stochastic column. The maximum is one of the mcl parameters, and
-it is typically set somewhere between 500 and 1500.
-Call the maximum <tt>K</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-mcl's time complexity is governed by the complexity of matrix squaring.
-There are two sub-algorithms to consider. The first is the
-algorithm responsible for assembling a new vector during matrix
-multiplication. This algorithm has worst case complexity <tt>O(K^2)</tt>.
-The pruning algorithm (which uses heap selection) has worst case complexity
-<tt>O(L*log(K))</tt>, where <tt>L</tt> is how large a newly computed matrix column can get
-before it is reduced to at most <tt>K</tt> entries. <tt>L</tt> is <i>bound by</i> the smallest
-of the two numbers <tt>N</tt> and <tt>K^2</tt> (the square of <tt>K</tt>), but on average
-<tt>L</tt> will be much smaller than that, as the presence of cluster structure aids in
-keeping the factor <tt>L</tt> low. [Related to this is the fact that clustering
-algorithms are actually used to compute matrix splittings that minimize
-the number of cross-computations when carrying out matrix
-multiplication among multiple processors.]
-In actual cases of heavy usage, <tt>L</tt> is of order in the tens of thousands, and
-<tt>K</tt> is in the order of several hundreds up to a thousand.</p>
-<p style="margin-bottom:0" class="asd_par">
-It is safe to say that in general the worst case complexity of mcl
-is of order O(N*K^2); for extremely tight and dense graphs this
-might become O(N*N*log(K)). Still, these are worst case estimates,
-and observed running times for actual usage are much better than that.
-(refer to faq <a class="intern" href="#stats">4.2</a>).</p>
-<p style="margin-bottom:0" class="asd_par">
-In this analysis, the number of iterations required by mcl was not
-included. It is nearly always far below 100. Only the first
-few (less than ten) iterations are genuinely time consuming, and they are
-usually responsible for more than 95 percent of the running time.</p>
-<p style="margin-bottom:0" class="asd_par">
-The process of removing the smallest entries of a vector is called
-pruning. mcl outputs a summary of this once it
-is done. More information is provided in the pruning section of the
-<a class="local sibling" href="mcl.html">mcl manual</a> and <a class="intern" href="#resource">Section 6</a>
-in this FAQ.</p>
-<p style="margin-bottom:0" class="asd_par">
-The space complexity is of order <tt>O(N*K)</tt>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="stats"></a> <a class="quiet" href="#toc-speed">4.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What statistics are available?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Few. Some experiments are described in <a class="intern" href="#pcfgcmce">[4]</a>, and
-<a class="intern" href="#eaflsdopf">[5]</a> mentions large graphs being clustered in very reasonable
-time. In protein clustering, <b>mcl</b> has been applied to graphs with up to one
-million nodes, and on high-end hardware such graphs can be clustered within
-a few hours.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="colsort"></a> <a class="quiet" href="#toc-speed">4.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Does this implementation need to sort vectors?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-No, it does not. You might expect that one needs to sort
-a vector in order to obtain the <tt>K</tt> largest entries, but a simpler
-mechanism called <i>heap selection</i> does the job nicely.
-Selecting the <tt>K</tt> largest entries from a set of <tt>L</tt> by sorting
-would require <tt>O(L*log(L))</tt> operations; heap selection
-requires <tt>O(L*log(K))</tt> operations.
-Alternatively, the <tt>K</tt> largest entries can be also be
-determined in <tt>O(N) + O(K log(K))</tt> asymptotic time by using partition
-selection (more <a target="_parent" class="extern" href="http://en.wikipedia.org/wiki/Selection_algorithm#Optimised_sorting_algorithms">here</a>
-and <a target="_parent" class="extern" href="http://wordaligned.org/articles/top-ten-percent">there</a>). It is
-possible to enable this mode of operaton in mcl with the option
-<b>--partition-selection</b>. However, benchmarking so far has shown this
-to be equivalent in speed to heap selection. This is explained by
-the bounded nature of <tt>K</tt> and <tt>L</tt> in practice.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="approx"></a> <a class="quiet" href="#toc-speed">4.4</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>mcl does not compute the ideal MCL process!</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Indeed it does not. What are the ramifications? Several entries in section
-<a class="intern" href="#resource">Resource tuning / accuracy</a> discuss this issue. For a synopsis,
-consider two ends of a spectrum.</p>
-<p style="margin-bottom:0" class="asd_par">
-On the one end, a graph that has very strong cluster structure,
-with clearly (and not necessarity fully) separated clusters. This
-mcl implementation will certainly retrieve those clusters if the
-graphs falls into <a class="intern" href="#whatkind">the category of graphs</a> for which
-mcl is applicable.
-On the other end, consider a graph that has only weak cluster
-structure superimposed on a background of a more or less random
-graph. There might sooner be a difference between the clustering
-that should ideally result and the one computed by mcl. Such
-a graph will have a large number of whimsical nodes that might end up
-either here or there, nodes that are of a peripheral nature,
-and for which the (cluster) destination is very sensitive to
-fluctutations in edge weights or algorithm parametrizations (any
-algorithm, not just mcl).</p>
-<p style="margin-bottom:0" class="asd_par">
-In short, the perturbation effect of the pruning process applied by mcl is a
-source of noise. It is small compared to the effect of
-changing the inflation parametrization or perturbing the edge weights. If
-the change is larger, this is because the computed process tends to converge
-prematurely, leading to finer-grained clusterings. As a result the
-clustering will be close to a <i>subclustering</i> of the clustering resulting
-from more conservative resource settings, and in that respect be consistent.
-All this can be measured using the program
-<a class="local" href="http://micans.org/mcl/man/clmdist.html">clm dist</a>. It is possible to
-offset such a change by slightly lowering the inflation parameter.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-There is the issue of very large and very dense graphs.
-The act of pruning will have a larger impact as graphs grow
-larger and denser.
-Obviously, mcl will have trouble dealing with such very large and very dense
-graphs — so will other methods.</p>
-<p style="margin-bottom:0" class="asd_par">
-Finally, there is the engineering approach, which offers the possibility of
-pruning a whole lot of speculation. Do the experiments with <b>mcl</b>, try it
-out, and see what's there to like and dislike.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="comparison"></a><a class="quiet" href="#toc-comparison">5</a><br>Comparison with other algorithms
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="xyzbetter"></a> <a class="quiet" href="#toc-comparison">5.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>I've read someplace that XYZ is much better than MCL</b>
-<p style="margin-top:0em; margin-bottom:0em">
-XYZ might well be the bees knees of all things clustering. Bear in mind
-though that comparing cluster algorithms is a very tricky affair.
-One particular trap is the following. Sometimes a new cluster algorithm is proposed based
-on some optimization criterion. The algorithm is then compared with
-previous algorithms (e.g. MCL). But how to compare? Quite often the
-comparison will be done by computing a criterion and astoundingly,
-quite often the chosen criterion is simply the optimization criterion again.
-<i>Of course</i> XYZ will do very well. It would be a very poor algorithm
-it if did not score well on its own optimization criterion, and it
-would be a very poor algorithm if it did not perform better than other
-algorithms which are built on different principles.</p>
-<p style="margin-bottom:0" class="asd_par">
-There are some further issues that have to be considered here.
-First, there is not a single optimization criterion that
-fully captures the notion of cluster structure, let alone best cluster
-structure. Second, leaving optimization approaches aside, it is not
-possible to speak of a best clustering. Best always depends on context -
-application field, data characteristics, scale (granularity), and
-practitioner to name but a few aspects.
-Accordingly, the best a clustering algorithm can hope for is to
-be a good fit for a certain class of problems. The class should not be
-too narrow, but no algorithm can cater for the broad spectre of
-problems for which clustering solutions are sought.
-The class of problems to which MCL is applicable is discussed
-in section <a class="intern" href="#kind">What kind of graphs</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="xyzslower"></a> <a class="quiet" href="#toc-comparison">5.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>I've read someplace that MCL is slow [compared with XYZ]</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Presumably, they did not know mcl, and did not read the parts
-in <a class="intern" href="#gcbfs">[1]</a> and <a class="intern" href="#cafg">[2]</a> that discuss implementation. Perhaps
-they assume or insist that the only way to implement MCL is to implement the
-ideal process. And there is always the genuine possibility
-of a <i>really</i> stupifyingly fast algorithm. It is certainly not the
-case that MCL has a time complexity of <tt>O(N^3)</tt> as is sometimes erroneously
-stated.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="resource"></a><a class="quiet" href="#toc-resource">6</a><br>Resource tuning / accuracy
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="wdymbrt"></a> <a class="quiet" href="#toc-resource">6.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What do you mean by resource tuning?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mcl</b> computes a process in which stochastic matrices are alternately
-expanded and inflated. Expansion is nothing but standard matrix
-multiplication, inflation is a particular way of rescaling the matrix
-entries.</p>
-<p style="margin-bottom:0" class="asd_par">
-Expansion causes problems in terms of both time and space. mcl works with
-matrices of dimension <tt>N</tt>, where <tt>N</tt> is the number of nodes in the input graph.
-If no precautions are taken, the number of entries in the mcl iterands
-(which are stochastic matrices) will soon approach the square of <tt>N</tt>. The
-time it takes to compute such a matrix will be proportional to the cube of
-<tt>N</tt>. If your input graph has 100.000 nodes, the memory requirements become
-infeasible and the time requirements become impossible.</p>
-<p style="margin-bottom:0" class="asd_par">
-What mcl does is perturbing the process it computes a little
-by removing the smallest entries — it keeps its matrices <i>sparse</i>.
-This is a natural thing to do, because the matrices are sparse in
-a weighted sense (a very high proportion of the stochastic mass
-is contained in relatively few entries), and the process converges
-to matrices that are extremely sparse, with usually no more than <tt>N</tt> entries.
-It is thus known that the MCL iterands are sparse in a weighted
-sense and are usually very close to truly sparse matrices.
-The way mcl perturbs its matrices is by the strategy
-of pruning, selection, and recovery that is extensively described
-in the <a class="local sibling" href="mcl.html">mcl manual page</a>.
-The question then is: What is the effect of this perturbation
-on the resulting clustering, i.e. how would the clustering
-resulting from a <i>perfectly computed</i> mcl process compare with
-the clustering I have on disk?
-<a class="intern" href="#pcmp">Faq entry 6.3</a> discusses this issue.</p>
-<p style="margin-bottom:0" class="asd_par">
-The amount of <i>resources</i> used by mcl is bounded in terms of the maximum
-number of neighbours a node is allowed to have during all computations.
-Equivalently, this is the maximum number of nonzero entries a matrix column
-can possibly have. This number, finally, is the maximum of the
-the values corresponding with the <b>-S</b> and <b>-R</b> options.
-The latter two are listed when using the <b>-z</b> option
-(see faq <a class="intern" href="#defaults">10.1</a>).</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq6.2"></a> <a class="quiet" href="#toc-resource">6.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I compute the maximum amount of RAM needed by mcl?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-It is rougly equal to</p>
-<div class="verbatim">2 * s * K * N</div>
-<p style="margin-top:0em; margin-bottom:0em">
-bytes, where 2 is the number of matrices held in memory by <b>mcl</b>, s is the
-size of a single cell (c.q. matrix entry or node/arc specification), <tt>N</tt> is
-the number of nodes in the input graph, and where <tt>K</tt> is the maximum of the
-values corresponding with the <b>-S</b> and <b>-R</b> options (and this
-assumes that the average node degree in the input graph does not exceed <tt>K</tt>
-either). The value of s can be found by using the <b>-z</b> option. It
-is listed in one of the first lines of the resulting output. s equals the
-size of an int plus the size of a float, which will be 8 on most systems.
-The estimate above will in most cases be way too pessimistic (meaning
-you do not need that amount of memory).</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-how-much-ram</b> option is provided by mcl for computing
-the bound given above. This options takes as argument the number of
-nodes in the input graph.</p>
-<p style="margin-bottom:0" class="asd_par">
-The theoretically more precise upper bound is slightly larger due to
-overhead. It is something like</p>
-<div class="verbatim">( 2 * s * (K + c)) * N</div>
-where c is 5 or so, but one should not pay attention to such a small
-difference anyway.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="pcmp"></a> <a class="quiet" href="#toc-resource">6.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How much does the mcl clustering differ from the clustering resulting
-from a perfectly computed MCL process?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-For graphs with up until a few thousand nodes a <i>perfectly computed</i>
-MCL process can be achieved by abstaining from pruning and doing
-full-blown matrix arithmetic. Of course, this still leaves the
-issue of machine precision, but let us wholeheartedly ignore that.</p>
-<p style="margin-bottom:0" class="asd_par">
-Such experiments give evidence (albeit incidental) that pruning is indeed
-really what it is thought to be - a small perturbation. In many cases, the
-'approximated' clustering is identical to the 'exact' clustering. In other
-cases, they are very close to each other in terms of the metric
-split/join distance as computed by <a class="local sibling" href="clmdist.html">clm dist</a>.
-Some experiments with randomly generated test graphs, clustering,
-and pruning are described in <a class="intern" href="#pcfgcmce">[4]</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-On a different level of abstraction, note that perturbations of the
-inflation parameter will also lead to perturbations in the resulting
-clusterings, and surely, large changes in the inflation parameter will in
-general lead to large shifts in the clusterings. Node/cluster pairs that
-are different for the approximated and the exact clustering will very
-likely correspond with nodes that are in a boundary region between two or
-more clusters anyway, as the perturbation is not likely to move a node from
-one core of attraction to another.</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#qsep">Faq entry 6.6</a> has more to say about this subject.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="enoughresources"></a> <a class="quiet" href="#toc-resource">6.4</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I know that I am using enough resources?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-In <b>mcl</b> parlance, this becomes <i>how do I know that my</i> <b>-scheme</b>
-<i>parameter is high enough</i> or more elaborately <i>how do I know
-that the values of the {-P, -S, -R, -pct} combo are high enough?</i></p>
-<p style="margin-bottom:0" class="asd_par">
-There are several aspects. First, watch the <i>jury marks</i> reported by <b>mcl</b>
-when it's done.
-The jury marks are three grades, each out of 100. They indicate how well
-pruning went. If the marks are in the seventies, eighties, or nineties, mcl
-is probably doing fine. If they are in the eighties or lower, try to see if
-you can get the marks higher by spending more resources (e.g. increase the
-parameter to the <b>-scheme</b> option).</p>
-<p style="margin-bottom:0" class="asd_par">
-Second, you can do multiple <b>mcl</b> runs for different resource schemes,
-and compare the resulting clusterings using <b>clm dist</b>. See
-the <a class="local sibling" href="clmdist.html">clmdist manual</a> for a case study.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="nmap"></a> <a class="quiet" href="#toc-resource">6.5</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Where is the mathematical analysis of this mcl pruning strategy?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-There is none. [add]</p>
-<p style="margin-bottom:0" class="asd_par">
-Ok, the next entry gives an engineer's rule of thumb.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="qsep"></a> <a class="quiet" href="#toc-resource">6.6</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What qualitative statements can be made about the effect of pruning?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-The more severe pruning is, the more the computed process will tend to
-converge prematurely. This will generally lead to finer-grained clusterings.
-In cases where pruning was severe, the <b>mcl</b> clustering will likely be closer
-to a clustering ideally resulting from another MCL process with higher
-inflation value, than to the clustering ideally resulting from the same MCL
-process. Strong support for this is found in a general observation
-illustrated by the following example. Suppose u is a stochastic vector
-resulting from expansion:</p>
-<div class="verbatim">u = 0.300 0.200 0.200 0.100 0.050 0.050 0.050 0.050</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Applying inflation with inflation value 2.0 to u gives</p>
-<div class="verbatim">v = 0.474 0.211 0.211 0.053 0.013 0.013 0.013 0.013</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Now suppose we first apply pruning to u such that the 3 largest entries
-0.300, 0.200 and 0.200 survive,
-throwing away 30 percent of the stochastic mass
-(which is quite a lot by all means).
-We rescale those three entries and obtain</p>
-<div class="verbatim">u' = 0.429 0.286 0.286 0.000 0.000 0.000 0.000 0.000</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Applying inflation with inflation value 2.0 to u' gives</p>
-<div class="verbatim">v' = 0.529 0.235 0.235 0.000 0.000 0.000 0.000 0.000</div>
-<p style="margin-top:0em; margin-bottom:0em">
-If we had applied inflation with inflation value 2.5 to u, we would
-have obtained</p>
-<div class="verbatim">v'' = 0.531 0.201 0.201 0.038 0.007 0.007 0.007 0.007</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The vectors v' and v'' are much closer to each other
-than the vectors v' and v, illustrating the general idea.</p>
-<p style="margin-bottom:0" class="asd_par">
-In practice, <b>mcl</b> should (on average) do much better than in this
-example.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq6.7"></a> <a class="quiet" href="#toc-resource">6.7</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>At different high resource levels my clusterings are not identical.
-How can I trust the output clustering?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Did you read all other entries in this section? That should have
-reassured you somewhat, except perhaps for
-<a class="intern" href="#nmap">Faq answer 6.5</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-You need not feel uncomfortable with the clusterings still being different
-at high resource levels, if ever so slightly. In all likelihood, there
-are anyway nodes which are not in any core of attraction, and that are on
-the boundary between two or more clusterings. They may go one way or
-another, and these are the nodes which will go different ways even at high
-resource levels. Such nodes may be stable in clusterings obtained for
-lower inflation values (i.e. coarser clusterings), in which the different
-clusters to which they are attracted are merged.</p>
-<p style="margin-bottom:0" class="asd_par">
-By the way, you do know all about <a class="local sibling" href="clmdist.html">clm dist</a>, don't you? Because the
-statement that clusterings are not identical should be quantified: <i>How
-much do they differ?</i> This issue is discussed in the <a class="local sibling" href="clmdist.html">clm dist</a> manual
-page — <b>clm dist</b> gives you a robust measure for the distance (dissimilarity)
-between two clusterings.</p>
-<p style="margin-bottom:0" class="asd_par">
-There are other means of gaining trust in a clustering, and there are
-different issues at play. There is the matter of how accurately this <b>mcl</b>
-computed the mcl process, and there is the matter of how well the chosen
-inflation parameter fits the data. The first can be judged by looking at
-the jury marks (<a class="intern" href="#enoughresources">faq 6.4</a>)
-and applying <b>clm dist</b> to different clusterings. The
-second can be judged by measurement (e.g. use <a class="local sibling" href="clminfo.html">clm info</a>) and/or
-inspection (use your judgment).</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="granularity"></a><a class="quiet" href="#toc-granularity">7</a><br>Tuning cluster granularity
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq7.1"></a> <a class="quiet" href="#toc-granularity">7.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I tune cluster granularity?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-There are several ways for influencing cluster granularity. These ways and
-their relative merits are successively discussed below.
-Reading <a class="local sibling" href="clmprotocols.html">clmprotocols</a> is also a good idea.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq7.2"></a> <a class="quiet" href="#toc-granularity">7.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>The effect of inflation on cluster granularity.</b>
-<p style="margin-top:0em; margin-bottom:0em">
-The main handle for changing inflation is the <b>-I</b> option. This is
-also <i>the</i> principal handle for regulating cluster granularity. Unless
-you are mangling huge graphs it could be the only <b>mcl</b> option you ever need
-besides the output redirection option <b>-o</b>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Increasing the value of <b>-I</b> will increase cluster granularity.
-Conceivable values are from 1.1 to 10.0 or so, but the range of suitable
-values will certainly depend on your input graph. For many graphs, 1.1 will
-be far too low, and for many other graphs, 8.0 will be far too high. You
-will have to find the right value or range of values by experimenting, using
-your judgment, and using measurement tools such as <a class="local sibling" href="clmdist.html">clm dist</a> and
-<a class="local sibling" href="clminfo.html">clm info</a>. A good set of values to start with is 1.4, 2 and 6.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="degree_granul"></a> <a class="quiet" href="#toc-granularity">7.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>The effect of node degrees on cluster granularity.</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Preferably the network should not have nodes of very high degree,
-that is, with exorbitantly many neighbours. Such nodes tend to
-obscure cluster structure and contribute to coarse clusters.
-The ways to combat this using <b>mcl</b> and sibling programs are documented
-in <a class="local sibling" href="clmprotocols.html">clmprotocols</a>. Briefly, they are the
-transformations <tt>#knn()</tt> and <tt>#ceilnb()</tt> available
-to <b>mcl</b>, <b>mcx alter</b> and several more programs.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="simil_granul"></a> <a class="quiet" href="#toc-granularity">7.4</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>The effect of edge weight differentiation on cluster granularity.</b>
-<p style="margin-top:0em; margin-bottom:0em">
-How similarities in the input graph were derived, constructed,
-adapted, filtered (et cetera) will affect cluster granularity.
-It is important that the similarities are honest;
-refer to <a class="intern" href="#goodinput">faq 3.8</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Another issue is that homogeneous similarities tend to result in more
-coarse-grained clusterings. You can make a set of similarities more
-homogeneous by applying some function to all of them, e.g. for all pairs of
-nodes (x y) replace S(x,y) by the square root, the logarithm, or some other
-convex function. Note that you need not worry about scaling, i.e. the
-possibly large changes in magnitude of the similarities. MCL is not affected
-by absolute magnitudes, it is only affected by magnitudes taken relative to
-each other.</p>
-<p style="margin-bottom:0" class="asd_par">
-As of version 03-154, mcl supports the pre-inflation <b>-pi</b> <i>f</i> option.
-Make a graph more homogeneous with respect to the weight
-function by using <b>-pi</b> with argument <i>f</i> somewhere
-in the interval [0,1] — 0.5 can be considered a reasonable first try.
-Make it less homogeneous by setting <i>f</i> somewhere in the interval [1,10].
-In this case 3 is a reasonable starting point.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="implement"></a><a class="quiet" href="#toc-implement">8</a><br>Implementing the MCL algorithm
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="faq8.1"></a> <a class="quiet" href="#toc-implement">8.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How easy is it to implement the MCL algorithm?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Very easy, if you will be doing small graphs only, say up to a few thousand
-entries at most. These are the basic ingredients:</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " >o</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Adding loops to the input graph, conversion to a stochastic matrix.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >o</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Matrix multiplication and matrix inflation.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >o</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The interpretation function mapping MCL limits onto clusterings.
-</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-These must be wrapped in a program that does graph input and cluster output,
-alternates multiplication (i.e. expansion) and inflation in a loop, monitors
-the matrix iterands thus found, quits the loop when convergence is detected,
-and interprets the last iterand.</p>
-<p style="margin-bottom:0" class="asd_par">
-Implementing matrix muliplication is a standard exercise. Implementing
-inflation is nearly trivial. The hardest part may actually be the
-interpretation function, because you need to cover the corner cases of
-overlap and attractor systems of cardinality greater than one. Note that
-MCL does not use intricate and expensive operations such as matrix inversion
-or matrix reductions.</p>
-<p style="margin-bottom:0" class="asd_par">
-In Mathematica or Maple, mcl should be doable in at most 100 lines of code.
-For perl you may need twice that amount. In lower level languages such as C
-or Fortran a basic MCL program may need a few hundred lines, but the largest
-part will probably be input/output and interpretation.</p>
-<p style="margin-bottom:0" class="asd_par">
-To illustrate all these points, mcl now ships with <a class="local" href="minimcl">minimcl</a>,
-a small perl script that implements mcl for educational purposes.
-Its structure is very simple and should be easy to follow.</p>
-<p style="margin-bottom:0" class="asd_par">
-Implementing the basic MCL algorithm makes a
-nice programming exercise. However, if you need an implementation that
-scales to several hundreds of thousands of nodes and possibly beyond, then
-your duties become much heavier. This is because one needs to prune MCL
-iterands (c.q. matrices) such that they remain sparse. This must be done
-carefully and preferably in such a way that a trade-off between speed,
-memory usage, and potential losses or gains in accuracy can be controlled
-via monitoring and logging of relevant characteristics.
-Some other points are
-i) support for threading via pthreads, openMP, or some other parallel
-programming API.
-ii) a robust and generic interpretation function is written in
-terms of weakly connected components.</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="overlap"></a><a class="quiet" href="#toc-overlap">9</a><br>Cluster overlap / MCL iterand cluster interpretation
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="olapintro"></a> <a class="quiet" href="#toc-overlap">9.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Introduction</b>
-A natural mapping exists of MCL iterands to DAGs
-(directed acyclic graphs). This is because MCL iterands are generally
-<i>diagonally positive semi-definite</i> — see <a class="intern" href="#supfg">[3]</a>.
-Such a DAG can be interpreted as a clustering, simply by taking
-as cores all endnodes (sinks) of the DAG, and by attaching to each
-core all the nodes that reach it. This procedure may result
-in clusterings containing overlap.
-<p style="margin-bottom:0" class="asd_par">
-In the MCL limit, the associated DAG has in general a very degenerated
-form, which induces overlap only on very rare occasions (see
-<a class="intern" href="#ccco">faq entry 9.2</a>).</p>
-<p style="margin-bottom:0" class="asd_par">
-Interpreting <b>mcl</b> iterands as clusterings may well be interesting.
-Few experiments have been done so far. It is clear though that
-early iterands generally contain the most overlap (when interpreted
-as clusterings). Overlap dissappears soon as the iterand
-index increases. For more information, consult the other entries
-in this section and the <a class="local sibling" href="clmimac.html">clmimac manual page</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="ccco"></a> <a class="quiet" href="#toc-overlap">9.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>Can the clusterings returned by mcl contain overlap?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-No. Clusterings resulting from the abstract MCL algorithm may in theory
-contain overlap, but the default behaviour in <b>mcl</b> is to remove it should it
-occur, by allocating the nodes in overlap to the first cluster in which they
-are seen. <b>mcl</b> will warn you if this occurs. This behaviour is switched
-off by supplying <b>--keep-overlap=yes</b>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Do note that overlap is mostly a theoretical possibility.
-It is conjectured that it requires the presence of very strong
-symmetries in the input graph, to the extent that there <i>exists
-an automorphism of the input graph mapping the overlapping part
-onto itself</i>.</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible to construct (highly symmetric) input graphs leading to
-cluster overlap. Examples of overlap in which a few nodes are involved are
-easy to construct; examples with many nodes are exceptionally hard to
-construct.</p>
-<p style="margin-bottom:0" class="asd_par">
-Clusterings associated with intermediate/early MCL iterands
-may very well contain overlap, see the
-<a class="intern" href="#olapintro">introduction in this section</a> and other entries.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="imac"></a> <a class="quiet" href="#toc-overlap">9.3</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I obtain the clusterings associated with MCL iterands?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-There are two options. If
-you are interested in clusterings containing overlap, you
-should go for the second. If not, use the first, but beware
-that the resulting clusterings may contain overlap.</p>
-<p style="margin-bottom:0" class="asd_par">
-The first solution is to use <b>-dump</b> <b>cls</b> (probably in conjunction
-with either <b>-L</b> or <b>-dumpi</b> in order to limit the number of
-matrices written). This will cause <b>mcl</b> to write the clustering generically
-associated with each iterand to file. The <b>-dumpstem</b> option may be
-convenient as well.</p>
-<p style="margin-bottom:0" class="asd_par">
-The second solution is to use the <b>-dump</b> <b>ite</b> option
-(<b>-dumpi</b> and <b>-dumpstem</b> may be of use again). This will
-cause <b>mcl</b> to write the intermediate iterands to file. After that, you can
-apply <a class="local sibling" href="clmimac.html">clm imac</a> (interpret matrix as clustering) to those iterands. <b>clm imac</b>
-has a <b>-strict</b> parameter which affects the mapping of matrices to
-clusterings. It takes a value between 0.0 and 1.0 as argument. The default is
-0.001 and corresponds with promoting overlap. Increasing the <b>-strict</b>
-value will generally result in clusterings containing less overlap. This
-will have the largest effect for early iterands; its effect will diminish as
-the iterand index increases.</p>
-<p style="margin-bottom:0" class="asd_par">
-When set to 0, the <b>-strict</b> parameter results in the clustering
-associated with the DAG associated with an MCL iterand as described
-in <a class="intern" href="#supfg">[3]</a>. This DAG is pruned (thus possibly resulting
-in less overlap in the clustering) by increasing the <b>-strict</b>
-parameter. [add]</p>
-</div>
-</div>
-
-<div align=center>
-<h3><a name="misc"></a><a class="quiet" href="#toc-misc">10</a><br>Miscellaneous
-</h3>
-</div>
-
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="defaults"></a> <a class="quiet" href="#toc-misc">10.1</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>How do I find the default settings of mcl?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-Use <b>-z</b> to find out the actual settings - it shows
-the settings as resulting from the command line options (e.g. the default
-settings if no other options are given).</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_compact"><div class=" item_leftalign nowrap " ><a name="next"></a> <a class="quiet" href="#toc-misc">10.2</a></div></div>
-<div class=" item_text " style="margin-left:2em">
-<b>What's next?</b>
-<p style="margin-top:0em; margin-bottom:0em">
-I'd like to port MCL to cluster computing, using one of the
-PVM, MPI, or openMP frameworks.
-For the 1.002 release, mcl's internals were rewritten to allow more general
-matrix computations. Among other things, mcl's data structures and primitive
-operations are now more suited to be employed in a distributed computing
-environment. However, much remains to be done before mcl can operate
-in such an environment.</p>
-<p style="margin-bottom:0" class="asd_par">
-If you feel that mcl should support some other standard matrix format,
-let us know.</p>
-</div>
-</div>
-
-<a name="bugs"></a>
-<h2>BUGS</h2>
-<p style="margin-bottom:0" class="asd_par">
-This FAQ tries to compromise between being concise and comprehensive. The
-collection of answers should preferably cover the universe of questions at a
-pleasant level of semantic granularity without too much overlap. It should
-offer value to people interested in clustering but without sound
-mathematical training. Therefore, if this FAQ has not failed somewhere,
-it must have failed.</p>
-<p style="margin-bottom:0" class="asd_par">
-Send criticism and missing questions for consideration to mcl-faq at
-micans.org.</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-<p style="margin-bottom:0" class="asd_par">
-mcl's home at <a class="extern" href="http://micans.org/mcl/">http://micans.org/mcl/</a>.</p>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a name="gcbfs">[1]</a>
-Stijn van Dongen. <i>Graph Clustering by Flow Simulation</i>.
-PhD thesis, University of Utrecht, May 2000.<br>
-<a class="extern" href="http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm">http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="cafg">[2]</a>
-Stijn van Dongen. <i>A cluster algorithm for graphs</i>.
-Technical Report INS-R0010, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="supfg">[3]</a>
-Stijn van Dongen. <i>A stochastic uncoupling process for graphs</i>.
-Technical Report INS-R0011, National Research Institute for Mathematics and
-Computer Science in the Netherlands, Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="pcfgcmce">[4]</a>
-Stijn van Dongen. <i>Performance criteria for graph clustering and Markov
-cluster experiments</i>. Technical Report INS-R0012, National Research
-Institute for Mathematics and Computer Science in the Netherlands,
-Amsterdam, May 2000.<br>
-<a class="extern" href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a name="eaflsdopf">[5]</a>
-Enright A.J., Van Dongen S., Ouzounis C.A.
-<i>An efficient algorithm for large-scale detection of protein families</i>,
-Nucleic Acids Research 30(7):1575-1584 (2002). </p>
-
-<a name="notes"></a>
-<h2>NOTES</h2>
-<p style="margin-bottom:0" class="asd_par">
-This page was generated from <b>ZOEM</b> manual macros,
-<a class="extern" href="http://micans.org/zoem">http://micans.org/zoem</a>. Both html and roff pages can be created
-from the same source without having to bother with all the usual conversion
-problems, while keeping some level of sophistication in the typesetting.
-<a class="local" href="mclfaq.ps">This</a> is the PostScript derived from the zoem
-troff output.</p>
-</body>
-</html>
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-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mclpipeline \- a generic pipeline for generating and scrutinizing mcl clusterings\&.
-
-\fBNOTE\fP
-.br
-\fBmcl\fP has acquired the ability to manipulate label input directly\&. This
-enables a very lightweight mechanism of generating clusterings by teaming up
-mcl with a lightweight parser\&. You might want to use this mechanism\&.
-Example invocations using the \fBmcxdeblast\fP BLAST parser are documented in the
-\fBmcl manual\fP\&.
-.SH SYNOPSIS
-
-\fBmclpipeline\fP [options] <file-name>
-.br
-
-where <file-name> is either the name of the data input file, or its base
-name\&. In the latter case the \fB--xi-dat\fP option is required\&. In case
-mclpipeline is indeed used to control all stages from the data input file
-onwards, usage will often be like this:
-
-.nf \fC
- mclpipeline [prepare options] --prepare-mcl <file-name>
- mclpipeline [cluster options 1] --start-mcl <file-name>
- mclpipeline [cluster options 2] --start-mcl <file-name>
- \&.\&. etc
-.fi \fR
-
-\fBmclpipeline\fP can also be used to control shorter pipelines, i\&.e\&. in
-case the input matrix was already created or in case pre-assembled parts
-of the input matrix were already created\&. In this case, usage will
-often be like this:
-
-.nf \fC
- mclpipeline [cluster options 1] --start-mcl=<fname>
- mclpipeline [cluster options 2] --start-mcl=<fname>
-or
- mclpipeline [assembly options] --start-assemble=<fname> --prepare-mcl
-.fi \fR
-
-\fBNOTE\fP
-.br
-It is possible to make mclpipeline output a large arrary
-of performance measures related to nodes and clusters
-in hyperlinked output by supplying the \fB--fmt-fancy\fP option\&.
-This can be useful if one wants to scrutinize a clustering in greater
-detail and navigate within the clustering\&. The output then includes
-listings of external nodes that are relevant/close to a given cluster,
-and vice versa, listings of external clusters that are relevant/close
-to a given node\&.
-
-Generating this more intricate output requires the presence of the \fBzoem\fP macro
-processor\&. Refer to the \fBSEE ALSO\fP section and the
-\fBclmformat manual\fP for more information on zoem\&. By default
-zoem is not required, and the return result is a file where each line contains
-a clustering consisting of tab-separated labels\&.
-
-If this program does not work as expected, please file a bug report with the
-developer and/or subscribe to mcl-devel as indicated on
-http://micans\&.org/mcl/\&. The problem will then be fixed\&.
-
-The full list of pipeline options is given below\&. Start simple,
-and if you need some behaviour, try to see if there is an option
-that fits your needs\&.
-If you use a wrapper pipeline such as \fBmclblastline(1)\fP, you
-can ignore the \fB--parser\fP and \fB--parser-tag\fP options
-as they are provided by the wrapper\&.
-
-\fBmclpipeline\fP
-\fB--parser=\fPapplication (\fIdata parser\fP)
-\fB--parser-tag=\fPstr (\fIparse option transporter\fP)
-
-\fB[--whatif\fP (\fIdo not execute\fP)\fB]\fP
-.br
-\fB[--start-assemble\fP (\fIskip parse stage\fP)\fB]\fP
-.br
-\fB[--start-mcl\fP (\fIskip earlier stages\fP)\fB]\fP
-.br
-\fB[--start-format\fP (\fIskip earlier stages\fP)\fB]\fP
-.br
-\fB[--prepare-mcl\fP (\fIdo preparatory stages\fP)\fB]\fP
-.br
-\fB[--help\fP (\fIsummary of options\fP)\fB]\fP
-.br
-\fB[--xi=\fPsuf (\fIstrip suf from input file\fP)\fB]\fP
-.br
-\fB[--xo-dat=\fPsuf (\fIattach suf to parse output\fP)\fB]\fP
-.br
-\fB[--xo-ass=\fPsuf (\fIattach suf to assembly output\fP)\fB]\fP
-.br
-\fB[--xi-mcl=\fPsuf (\fIuse with --start-mcl\fP)\fB]\fP
-.br
-\fB[--xo-mcl=\fPsuf (\fIreplace mcl output suffix\fP)\fB]\fP
-.br
-\fB[--xa-mcl=\fPstr (\fIappend to mcl output suffix\fP)\fB]\fP
-.br
-\fB[--xe-mcl=\fPsuf (\fIappend to mcl output\fP)\fB]\fP
-.br
-\fB[--xo-fmt=\fPsuf (\fIattach suf to clmformat output\fP)\fB]\fP
-.br
-\fB[--ass-repeat=\fPstr (\fIassembly repeat option\fP)\fB]\fP
-.br
-\fB[--ass-nomap\fP (\fIignore map file\fP)\fB]\fP
-.br
-\fB[--ass-opt=\fPval (\fIassembly option transporter\fP)\fB]\fP
-.br
-\fB[--mcl-te=\fPnum (\fI#expansion threads\fP)\fB]\fP
-.br
-\fB[--mcl-I=\fPfloat (\fImcl inflation value\fP)\fB]\fP
-.br
-\fB[--mcl-i=\fPfloat (\fImcl initial inflation value\fP)\fB]\fP
-.br
-\fB[--mcl-l=\fPfloat (\fImcl initial loop length\fP)\fB]\fP
-.br
-\fB[--mcl-c=\fPfloat (\fImcl center value\fP)\fB]\fP
-.br
-\fB[--mcl-pi=\fPfloat (\fImcl pre-inflation value\fP)\fB]\fP
-.br
-\fB[--mcl-scheme=\fPi (\fImcl scheme index\fP)\fB]\fP
-.br
-\fB[--mcl-o=\fPfname (\fIdo not use\fP)\fB]\fP
-.br
-\fB[--mcl-opt=\fPval (\fImcl option transporter\fP)\fB]\fP
-.br
-\fB[--fmt-lump-count=\fPnum (\fIcollect formatted output\fP)\fB]\fP
-.br
-\fB[--fmt-opt\fP val (\fIclmformat option transporter\fP)\fB]\fP
-.br
-\fB[--fmt-tab\fP fname (\fIuse this tab file\fP)\fB]\fP
-.br
-\fB[--fmt-notab\fP (\fIignore tab file\fP)\fB]\fP
-.br
-<file-name>
-.SH DESCRIPTION
-
-\fBmclpipeline\fP encapsulates a sequence of programs to be run on some
-input data in order to obtain clusterings and formatted output
-representing the clusterings, while maintaining unique file names
-and file name ensembles corresponding with differently parametrized runs\&.
-
-The script can behave in several ways\&. By default, the pipeline
-consists of the stages of \fIparsing\fP, \fIassembly\fP,
-\fIclustering\fP, and \fIformatting\fP\&.
-The parsing stage is to be
-represented by some parser script obeying the interface
-rules described below\&. The assembly stage is done by
-\fBmcxassemble(1)\fP, the clustering stage is done by \fBmcl(1)\fP,
-and the formatting stage is done by \fBclmformat(1)\fP\&.
-
-The script can also be put to simpler uses, e\&.g\&. letting the script take
-care of unique file names for differently parametrized mcl runs\&. In this
-case there is no need to specify either the parser or the data file, and
-subsequent invocations might look like this:
-
-.nf \fC
-
- mclpipeline --start-mcl=<fname> --mcl-I=1\&.6 --mcl-scheme=4
- mclpipeline --start-mcl=<fname> --mcl-I=2\&.0 --mcl-scheme=4
- mclpipeline --start-mcl=<fname> --mcl-I=2\&.4 --mcl-scheme=4
- \&.\&. etc
-.fi \fR
-
-It is easiest if for each parser a wrapper script is written
-encapsulating the parser and \fBmclpipeline\fP\&. A mechanism is provided
-through which mclpipeline can recognize options that are meant to be
-passed to the parser\&. An example of such a wrapper script is the BLAST
-pipeline \fBmclblastline\fP that basically calls mclpipeline with the
-parameters \fB--parser\fP=\fBmcxdeblast\fP \fB--parser-tag\fP=\fBblast\fP\&.
-In this case the parser is \fBmcxdeblast\fP, and mclpipeline will
-pass any options of the forms \fB--blast-foo\fP and \fB--blast-bar=zut\fP
-to the parser (respectively as \fB--foo\fP and \fB--bar=zut\fP)\&.
-
-For a given data set the stages of parsing and assembling
-will often not need to be repeated, especially if there
-is a well established way of creating a matrix from
-the input data\&. In this case, usage
-will look like
-
-.nf \fC
-
- mclpipeline [parse/assembly options] --prepare-mcl <file-name>
- mclpipeline [cluster options 1] --start-mcl <file-name>
- mclpipeline [cluster options 2] --start-mcl <file-name>
- mclpipeline [cluster options 3] --start-mcl <file-name>
- \&.\&.\&.
-.fi \fR
-
-Note that \fBmclpipeline\fP will store the output of those runs
-in unique file names derived from the parametrizations\&.
-
-There are some options that affect the file names of intermediate
-results\&. In the above setup of repeated runs, if used in one run,
-they must be used in all runs, as \fBmclpipeline\fP uses them to compute the
-file names it needs\&.
-For the setup above, these options are
-\fB--xi\fP=\fIsuf\fP,
-\fB--xo-dat\fP=\fIsuf\fP, and
-\fB--xo-ass\fP=\fIsuf\fP\&.
-
-There are other ways of resuming the pipeline, and one must always take care
-that options starting with \fB--xi-\fP, \fB--xo-\fP, \fB--xa\fP, or
-\fB--xe\fP are repeated among preparatory and subsequent runs\&.
-These tags respectively mnemonize \fIextension in\fP, \fIextension out\fP,
-\fIextension append\fP, and \fIextension extra\fP\&.
-
-Should one want to experiment with various ways of creating input
-matrices, then \fBmclpipeline\fP supplies options to create unique file
-names and file name ensembles corresponding with different setups and
-parametrizations\&. These are \fB--xo-dat\fP=\fIsuf\fP for the parsing
-stage and \fB--xo-ass\fP=\fIsuf\fP for the assembly stage\&. mclpipeline
-\fIautomatically\fP generates unique file names for the cluster results,
-but it does not do so for the parse and assembly results\&.
-
-\fBParser interface requirements\fP
-.br
-The parser should recognize its last argument as a file name
-or as the base name of a file\&.
-It should produce the files \fCbase\&.raw\fP, \fCbase\&.hdr\fP,
-and preferably \fCbase\&.tab\fP and \fCbase\&.map\fP, where the base name
-\fCbase\fP is determined as described below\&.
-
-\fBmclpipeline\fP will pass its last argument <file-name> to the parser\&.
-The parser should recognize the \fB--xi-dat\fP=\fIsuf\fP
-and \fB--xo-dat\fP=\fIsuf\fP options\&. If the first is present,
-it should try to strip <file-name> of the suffix specified in
-the value and use the result as the initial part of the base name
-for the files it constructs\&. If stripping does not succeed, it
-must interpret <file-name> as the base name and append the suffix
-in order to construct the name of the file it will try to read\&.
-If the \fB--xo-dat\fP=\fIsuf\fP option is present, it must append the
-suffix specified in the value to the base part as described above\&.
-The result is then the full base name to which the \fCraw\fP, \fChdr\fP,
-and other suffixes will be appended\&.
-
-\fBParser interface examples\fP
-.br
-
-.nf \fC
-<parser> --xi-dat=abc --xo-dat=xyz foo
- * parser reads foo\&.abc, writes foo\&.xyz\&.raw, foo\&.xyz\&.hdr et cetera\&.
-<parser> --xi-dat=abc --xo-dat=xyz foo\&.abc
- * idem
-<parser> --xo-dat=xyz foo\&.abc
- * parser reads foo\&.abc, writes foo\&.abc\&.xyz\&.raw et cetera\&.
-<parser> --xi-dat=abc foo\&.abc
- * parser reads foo\&.abc, writes foo\&.raw, foo\&.hdr et cetera\&.
-<parser> foo\&.abc
- * parser reads foo\&.abc, writes foo\&.abc\&.raw, foo\&.abc\&.hdr et cetera\&.
-.fi \fR
-
-\fBOutput file names construction\fP
-.br
-The files of primary interest are the mcl output file and
-the formatted output produced by clmformat\&.
-The pipeline constructs a file name for the mcl output
-in which several parameters are encoded\&. The first
-part of the file name is either the base name for the assembly
-stage, or simply the name of the input file, depending on
-whether the option \fB--xo-ass\fP=\fIsuf\fP was used or not\&.
-
-A suffix encoding key-value pairs is appended\&. By default
-it has the form \fCI\&.\&.s\&.\fP, e\&.g\&. \fCI20s2\fP\&. The latter examples
-denotes primary inflation value 2\&.0 and scheme 2\&.
-The pipeline will automatically append several other mcl parameters
-if they are used\&. These correspond with the pipeline options
-\fB--mcl-i\fP=\fIf\fP, \fB--mcl-l\fP=\fIi\fP, \fB--mcl-c\fP=\fIf\fP,
-and \fB--mcl-pi\fP=\fIf\fP,
-which in turn correspond with the mcl options \fB-i\fP\ \&\fIf\fP,
-\fB-l\fP\ \&\fIi\fP, \fB-c\fP\ \&\fIf\fP, and \fB-pi\fP\ \&\fIf\fP\&.
-The order of appending is alphabetical with capitals preceding
-lowercase, so a full example is \fCI25c30i35l2pi28s3\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB--whatif\fP (\fIdo not execute\fP)"
-\&
-.br
-Shows only what would be done without executing it\&.
-Hugely useful!
-.in -2m
-
-.ZI 2m "\fB--start-assemble\fP (\fIskip parse stage\fP)"
-\&
-.br
-Skip the parse stage, assume the necessary files have been created in a
-previous run\&.
-.in -2m
-
-.ZI 2m "\fB--prepare-mcl\fP (\fIdo preparatory stages\fP)"
-\&
-.br
-Do the parsing and assembly stage, then quit\&. Useful if you
-want to do multiple cluster runs for a given graph - use
-\fB--start-mcl\fP
-.in -2m
-
-.ZI 2m "\fB--start-mcl\fP (\fIskip earlier stages\fP)"
-\&
-.br
-Immediately start the mcl stage\&.
-Assume the necessary files have been created in a previous run\&.
-
-\fBNOTE\fP
-.br
-This option can be used as \fB--start-mcl\fP=\fIfname\fP\&.
-In this case, no final file name argument need be given, and
-mcl will use \fIfname\fP as the file name for its input\&.
-
-The difference with \fB--start-mcl\fP is that the latter
-will assume it is picking up the results of a previous run\&.
-The names of those results might include suffixes corresponding
-with the parse and assembly stage (cf\&. \fB--xo-dat\fP and
-\fB--xo-ass\fP)\&.
-If you are not clear on this (and you should not be), exercise
-the \fB--whatif\fP option to be sure\&.
-.in -2m
-
-.ZI 2m "\fB--start-format\fP (\fIskip earlier stages\fP)"
-\&
-.br
-Immediately start the format stage\&.
-Assume the necessary files have been created in a previous run\&.
-.in -2m
-
-.ZI 2m "\fB--help\fP (\fIsummary of options\fP)"
-\&
-.br
-Print a terse summary of options\&.
-.in -2m
-
-.ZI 2m "\fB--xi\fP suf (\fIstrip suffix from data file\fP)"
-\&
-.br
-In normal usage, this will strip the specified suffix from the data file
-to obtain the base name for further output\&.
-When used with \fB--start-mcl\fP=\fIfname\fP the same behaviour is applied
-to the mcl input file name specified in \fIfname\fP\&.
-.in -2m
-
-.ZI 2m "\fB--xo-dat\fP suf (\fIattach suf to parse output\fP)"
-\&
-.br
-This suffix will be attached to the base name of the parse output\&.
-It can be used to distinguish between different parse parametrizations
-if this is applicable\&.
-.in -2m
-
-.ZI 2m "\fB--xo-ass\fP suf (\fIattach suf to assembly output\fP)"
-\&
-.br
-This suffix will be attached to the base name of the assembly output\&.
-It can be used to distinguish between different assembly parametrizations
-if this is applicable\&.
-.in -2m
-
-.ZI 2m "\fB--xo-mcl\fP suf (\fIreplace mcl output suffix\fP)"
-\&
-.br
-This suffix will be used instead of the suffix by default created
-by the pipeline\&.
-.in -2m
-
-.ZI 2m "\fB--xa-mcl\fP str (\fIappend to mcl output suffix\fP)"
-\&
-.br
-This string will be appended to the suffix by default created
-by the pipeline\&.
-.in -2m
-
-.ZI 2m "\fB--xe-mcl\fP suf (\fIappend to mcl output\fP)"
-\&
-.br
-This string will be appended as a single suffix to the output base
-name before mclpipeline appends its own suffix\&.
-.in -2m
-
-.ZI 2m "\fB--xo-fmt\fP suf (\fIattach suf to clmformat output\fP)"
-\&
-.br
-This suffix will be used instead of the suffix by default used
-by the formatting stage\&.
-.in -2m
-
-.ZI 2m "\fB--ass-repeat\fP str (\fIassembly repeat option\fP)"
-\&
-.br
-Corresponds with the \fBmcxassemble\fP \fB-r\fP\ \&\fImode\fP option\&.
-Refer to the \fBmcxassemble(1)\fP manual\&.
-.in -2m
-
-.ZI 2m "\fB--ass-opt\fP val (\fIassembly option transporter\fP)"
-\&
-.br
-Transfer \fB-opt\fP\ \&\fIval\fP to \fBmcxassemble\fP\&.
-.in -2m
-
-.ZI 2m "\fB--ass-nomap\fP (\fIignore map file\fP)"
-\&
-.br
-Either no map file is present or it should be ignored\&.
-For parsers that don\&'t write map files\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-I\fP float (\fImcl inflation value\fP)"
-\&
-.br
-The (main) inflation value mcl should use\&.
-\fIThis is the primary mcl option\fP\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-scheme\fP i (\fImcl scheme index\fP)"
-\&
-.br
-The scheme index to use\&. This options is also important\&.
-Refer to the \fBmcl(1)\fP manual\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-te\fP num (\fI#expansion threads\fP)"
-\&
-.br
-The number of threads \fBmcl\fP should use\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-i\fP float (\fImcl initial inflation value\fP)"
-\&
-.br
-The initial inflation value mcl should use\&.
-Only for fine-tuning or testing\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-l\fP float (\fImcl initial loop length\fP)"
-\&
-.br
-The length of the loop in which initial inflation
-is applied\&. By default zero\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-c\fP float (\fImcl center value\fP)"
-\&
-.br
-The center value\&. One may attempt to affect granularity
-by exercising this option, which controls the loop weights
-in the input matrix\&. Refer to the \fBmcl(1)\fP manual\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-pi\fP float (\fImcl pre-inflation value\fP)"
-\&
-.br
-Pre-inflation, another option which may possibly affect granularity by
-changing the input matrix\&. It makes the edge weight
-distribution either more or less homogeneous\&.
-Refer to the \fBmcl(1)\fP manual\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-o\fP fname (\fIdo not use\fP)"
-\&
-.br
-Set the mcl output name\&.
-.in -2m
-
-.ZI 2m "\fB--mcl-opt\fP val (\fImcl option transporter\fP)"
-\&
-.br
-Transfer \fB-opt\fP\ \&\fIval\fP to \fBmcl\fP\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-dump-stats\fP (\fIadd simple measures to dump file\fP)"
-\&
-.br
-This adds some simple performance measures to the dump file\&. For each
-cluster, five columns proceed the label listing\&. These are the cluster ID,
-the number of elements in the cluster, the projection (percentage of
-within-cluster edge weight relative to total outgoing edge weight), the
-efficiency of the cluster (which is the average of the efficiency of all its
-nodes), and the maximum efficiency (average of the max-efficiency of all the
-nodes)\&. Look into the \fBclmformat manual\fP for more
-information on and references to the efficiency measures\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-fancy\fP (\fIcreate detailed output (requires zoem)\fP)"
-\&
-.br
-Creates extensive description of node/cluster and cluster/cluster
-relationships\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-lump-count\fP num (\fIcollect formatted output\fP)"
-\&
-.br
-Collect clusters in the same file until the total number
-of nodes has exceeded \fInum\fP (in the formatted output)\&.
-Only meaninful when \fB--fmt-fancy\fP is given\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-tab\fP (\fIuse this tab file\fP)"
-\&
-.br
-Explicitly specify the tab file to use\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-notab\fP (\fIignore tab file\fP)"
-\&
-.br
-Either no tab file is present or it should be ignored\&.
-For parsers that don\&'t write tab files\&.
-.in -2m
-
-.ZI 2m "\fB--fmt-opt\fP val (\fIclmformat option transporter\fP)"
-\&
-.br
-Transfer \fB-opt\fP\ \&\fIval\fP to \fBclm format\fP\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen
-.SH SEE ALSO
-
-\fBmcxdeblast(1)\fP, \fBmclblastline(1)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
-
-With default settings, \fBmclpipeline\fP depends on the presence
-of \fBzoem\fP\&. It can be obtained from
-http://micans\&.org/zoem/ \&.
diff --git a/doc/mclpipeline.html b/doc/mclpipeline.html
deleted file mode 100644
index 3fb29ba..0000000
--- a/doc/mclpipeline.html
+++ /dev/null
@@ -1,620 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
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-body
-{ text-align: justify;
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-<title>The mclpipeline manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclpipeline.ps"><b>mclpipeline</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclpipeline — a generic pipeline for generating and scrutinizing mcl clusterings.</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-<b>mcl</b> has acquired the ability to manipulate label input directly. This
-enables a very lightweight mechanism of generating clusterings by teaming up
-mcl with a lightweight parser. You might want to use this mechanism.
-Example invocations using the <b>mcxdeblast</b> BLAST parser are documented in the
-<a class="local sibling" href="mcl.html">mcl manual</a>.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclpipeline</b> [options] <file-name><br>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-where <file-name> is either the name of the data input file, or its base
-name. In the latter case the <b>--xi-dat</b> option is required. In case
-mclpipeline is indeed used to control all stages from the data input file
-onwards, usage will often be like this:
-</p>
-<div class="verbatim"> mclpipeline [prepare options] --prepare-mcl <file-name>
- mclpipeline [cluster options 1] --start-mcl <file-name>
- mclpipeline [cluster options 2] --start-mcl <file-name>
- .. etc
-</div>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclpipeline</b> can also be used to control shorter pipelines, i.e. in
-case the input matrix was already created or in case pre-assembled parts
-of the input matrix were already created. In this case, usage will
-often be like this:
-</p>
-<div class="verbatim"> mclpipeline [cluster options 1] --start-mcl=<fname>
- mclpipeline [cluster options 2] --start-mcl=<fname>
-or
- mclpipeline [assembly options] --start-assemble=<fname> --prepare-mcl
-</div>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-It is possible to make mclpipeline output a large arrary
-of performance measures related to nodes and clusters
-in hyperlinked output by supplying the <b>--fmt-fancy</b> option.
-This can be useful if one wants to scrutinize a clustering in greater
-detail and navigate within the clustering. The output then includes
-listings of external nodes that are relevant/close to a given cluster,
-and vice versa, listings of external clusters that are relevant/close
-to a given node.</p>
-<p style="margin-bottom:0" class="asd_par">
-Generating this more intricate output requires the presence of the <b>zoem</b> macro
-processor. Refer to the <a class="intern" href="#seealso">SEE ALSO</a> section and the
-<a class="local sibling" href="clmformat.html">clmformat manual</a> for more information on zoem. By default
-zoem is not required, and the return result is a file where each line contains
-a clustering consisting of tab-separated labels.</p>
-<p style="margin-bottom:0" class="asd_par">
-If this program does not work as expected, please file a bug report with the
-developer and/or subscribe to mcl-devel as indicated on
-<a class="extern" href="http://micans.org/mcl/">http://micans.org/mcl/</a>. The problem will then be fixed.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The full list of pipeline options is given below. Start simple,
-and if you need some behaviour, try to see if there is an option
-that fits your needs.
-If you use a wrapper pipeline such as <a class="local sibling" href="mclblastline.html">mclblastline</a>, you
-can ignore the <b>--parser</b> and <b>--parser-tag</b> options
-as they are provided by the wrapper.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclpipeline</b>
-<a class="intern" href="#opt--parser"><b>--parser=</b>application (<i>data parser</i>)</a>
-<a class="intern" href="#opt--parser-tag"><b>--parser-tag=</b>str (<i>parse option transporter</i>)</a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#opt--whatif"><b>[--whatif</b> (<i>do not execute</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--start-assemble"><b>[--start-assemble</b> (<i>skip parse stage</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--start-mcl"><b>[--start-mcl</b> (<i>skip earlier stages</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--start-format"><b>[--start-format</b> (<i>skip earlier stages</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--prepare-mcl"><b>[--prepare-mcl</b> (<i>do preparatory stages</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--help"><b>[--help</b> (<i>summary of options</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xi"><b>[--xi=</b>suf (<i>strip suf from input file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xo-dat"><b>[--xo-dat=</b>suf (<i>attach suf to parse output</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xo-ass"><b>[--xo-ass=</b>suf (<i>attach suf to assembly output</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xi-mcl"><b>[--xi-mcl=</b>suf (<i>use with --start-mcl</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xo-mcl"><b>[--xo-mcl=</b>suf (<i>replace mcl output suffix</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xa-mcl"><b>[--xa-mcl=</b>str (<i>append to mcl output suffix</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xe-mcl"><b>[--xe-mcl=</b>suf (<i>append to mcl output</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--xo-fmt"><b>[--xo-fmt=</b>suf (<i>attach suf to clmformat output</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--ass-repeat"><b>[--ass-repeat=</b>str (<i>assembly repeat option</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--ass-nomap"><b>[--ass-nomap</b> (<i>ignore map file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--ass-opt"><b>[--ass-opt=</b>val (<i>assembly option transporter</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-te"><b>[--mcl-te=</b>num (<i>#expansion threads</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-I"><b>[--mcl-I=</b>float (<i>mcl inflation value</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-i"><b>[--mcl-i=</b>float (<i>mcl initial inflation value</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-l"><b>[--mcl-l=</b>float (<i>mcl initial loop length</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-c"><b>[--mcl-c=</b>float (<i>mcl center value</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-pi"><b>[--mcl-pi=</b>float (<i>mcl pre-inflation value</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-scheme"><b>[--mcl-scheme=</b>i (<i>mcl scheme index</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-o"><b>[--mcl-o=</b>fname (<i>do not use</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--mcl-opt"><b>[--mcl-opt=</b>val (<i>mcl option transporter</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--fmt-lump-count"><b>[--fmt-lump-count=</b>num (<i>collect formatted output</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--fmt-opt"><b>[--fmt-opt</b> val (<i>clmformat option transporter</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--fmt-tab"><b>[--fmt-tab</b> fname (<i>use this tab file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--fmt-notab"><b>[--fmt-notab</b> (<i>ignore tab file</i>)<b>]</b></a><br>
-<file-name>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclpipeline</b> encapsulates a sequence of programs to be run on some
-input data in order to obtain clusterings and formatted output
-representing the clusterings, while maintaining unique file names
-and file name ensembles corresponding with differently parametrized runs.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The script can behave in several ways. By default, the pipeline
-consists of the stages of <i>parsing</i>, <i>assembly</i>,
-<i>clustering</i>, and <i>formatting</i>.
-The parsing stage is to be
-represented by some parser script obeying the interface
-rules described below. The assembly stage is done by
-<a class="local sibling" href="mcxassemble.html">mcxassemble</a>, the clustering stage is done by <a class="local sibling" href="mcl.html">mcl</a>,
-and the formatting stage is done by <a class="local sibling" href="clmformat.html">clmformat</a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The script can also be put to simpler uses, e.g. letting the script take
-care of unique file names for differently parametrized mcl runs. In this
-case there is no need to specify either the parser or the data file, and
-subsequent invocations might look like this:
-</p>
-<div class="verbatim">
- mclpipeline --start-mcl=<fname> --mcl-I=1.6 --mcl-scheme=4
- mclpipeline --start-mcl=<fname> --mcl-I=2.0 --mcl-scheme=4
- mclpipeline --start-mcl=<fname> --mcl-I=2.4 --mcl-scheme=4
- .. etc
-</div>
-<p style="margin-bottom:0" class="asd_par">
-It is easiest if for each parser a wrapper script is written
-encapsulating the parser and <b>mclpipeline</b>. A mechanism is provided
-through which mclpipeline can recognize options that are meant to be
-passed to the parser. An example of such a wrapper script is the BLAST
-pipeline <b>mclblastline</b> that basically calls mclpipeline with the
-parameters <b>--parser</b>=<b>mcxdeblast</b> <b>--parser-tag</b>=<b>blast</b>.
-In this case the parser is <b>mcxdeblast</b>, and mclpipeline will
-pass any options of the forms <b>--blast-foo</b> and <b>--blast-bar=zut</b>
-to the parser (respectively as <b>--foo</b> and <b>--bar=zut</b>).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For a given data set the stages of parsing and assembling
-will often not need to be repeated, especially if there
-is a well established way of creating a matrix from
-the input data. In this case, usage
-will look like
-</p>
-<div class="verbatim">
- mclpipeline [parse/assembly options] --prepare-mcl <file-name>
- mclpipeline [cluster options 1] --start-mcl <file-name>
- mclpipeline [cluster options 2] --start-mcl <file-name>
- mclpipeline [cluster options 3] --start-mcl <file-name>
- ...
-</div>
-<p style="margin-bottom:0" class="asd_par">
-Note that <b>mclpipeline</b> will store the output of those runs
-in unique file names derived from the parametrizations.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-There are some options that affect the file names of intermediate
-results. In the above setup of repeated runs, if used in one run,
-they must be used in all runs, as <b>mclpipeline</b> uses them to compute the
-file names it needs.
-For the setup above, these options are
-<b>--xi</b>=<i>suf</i>,
-<b>--xo-dat</b>=<i>suf</i>, and
-<b>--xo-ass</b>=<i>suf</i>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-There are other ways of resuming the pipeline, and one must always take care
-that options starting with <b>--xi-</b>, <b>--xo-</b>, <b>--xa</b>, or
-<b>--xe</b> are repeated among preparatory and subsequent runs.
-These tags respectively mnemonize <i>extension in</i>, <i>extension out</i>,
-<i>extension append</i>, and <i>extension extra</i>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Should one want to experiment with various ways of creating input
-matrices, then <b>mclpipeline</b> supplies options to create unique file
-names and file name ensembles corresponding with different setups and
-parametrizations. These are <b>--xo-dat</b>=<i>suf</i> for the parsing
-stage and <b>--xo-ass</b>=<i>suf</i> for the assembly stage. mclpipeline
-<i>automatically</i> generates unique file names for the cluster results,
-but it does not do so for the parse and assembly results.
-</p>
-<p style="margin-bottom:0"><b>Parser interface requirements</b><br>
-The parser should recognize its last argument as a file name
-or as the base name of a file.
-It should produce the files <tt>base.raw</tt>, <tt>base.hdr</tt>,
-and preferably <tt>base.tab</tt> and <tt>base.map</tt>, where the base name
-<tt>base</tt> is determined as described below.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclpipeline</b> will pass its last argument <file-name> to the parser.
-The parser should recognize the <b>--xi-dat</b>=<i>suf</i>
-and <b>--xo-dat</b>=<i>suf</i> options. If the first is present,
-it should try to strip <file-name> of the suffix specified in
-the value and use the result as the initial part of the base name
-for the files it constructs. If stripping does not succeed, it
-must interpret <file-name> as the base name and append the suffix
-in order to construct the name of the file it will try to read.
-If the <b>--xo-dat</b>=<i>suf</i> option is present, it must append the
-suffix specified in the value to the base part as described above.
-The result is then the full base name to which the <tt>raw</tt>, <tt>hdr</tt>,
-and other suffixes will be appended.
-</p>
-<p style="margin-bottom:0"><b>Parser interface examples</b><br></p>
-<div class="verbatim"><parser> --xi-dat=abc --xo-dat=xyz foo
- * parser reads foo.abc, writes foo.xyz.raw, foo.xyz.hdr et cetera.
-<parser> --xi-dat=abc --xo-dat=xyz foo.abc
- * idem
-<parser> --xo-dat=xyz foo.abc
- * parser reads foo.abc, writes foo.abc.xyz.raw et cetera.
-<parser> --xi-dat=abc foo.abc
- * parser reads foo.abc, writes foo.raw, foo.hdr et cetera.
-<parser> foo.abc
- * parser reads foo.abc, writes foo.abc.raw, foo.abc.hdr et cetera.
-</div>
-<p style="margin-bottom:0"><b>Output file names construction</b><br>
-The files of primary interest are the mcl output file and
-the formatted output produced by clmformat.
-The pipeline constructs a file name for the mcl output
-in which several parameters are encoded. The first
-part of the file name is either the base name for the assembly
-stage, or simply the name of the input file, depending on
-whether the option <b>--xo-ass</b>=<i>suf</i> was used or not.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-A suffix encoding key-value pairs is appended. By default
-it has the form <tt>I..s.</tt>, e.g. <tt>I20s2</tt>. The latter examples
-denotes primary inflation value 2.0 and scheme 2.
-The pipeline will automatically append several other mcl parameters
-if they are used. These correspond with the pipeline options
-<b>--mcl-i</b>=<i>f</i>, <b>--mcl-l</b>=<i>i</i>, <b>--mcl-c</b>=<i>f</i>,
-and <b>--mcl-pi</b>=<i>f</i>,
-which in turn correspond with the mcl options <b>-i</b> <i>f</i>,
-<b>-l</b> <i>i</i>, <b>-c</b> <i>f</i>, and <b>-pi</b> <i>f</i>.
-The order of appending is alphabetical with capitals preceding
-lowercase, so a full example is <tt>I25c30i35l2pi28s3</tt>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--whatif"></a><b>--whatif</b> (<i>do not execute</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shows only what would be done without executing it.
-Hugely useful!
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--start-assemble"></a><b>--start-assemble</b> (<i>skip parse stage</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Skip the parse stage, assume the necessary files have been created in a
-previous run.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--prepare-mcl"></a><b>--prepare-mcl</b> (<i>do preparatory stages</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Do the parsing and assembly stage, then quit. Useful if you
-want to do multiple cluster runs for a given graph - use
-<b>--start-mcl</b>
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--start-mcl"></a><b>--start-mcl</b> (<i>skip earlier stages</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Immediately start the mcl stage.
-Assume the necessary files have been created in a previous run.
-</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-This option can be used as <b>--start-mcl</b>=<i>fname</i>.
-In this case, no final file name argument need be given, and
-mcl will use <i>fname</i> as the file name for its input.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The difference with <b>--start-mcl</b> is that the latter
-will assume it is picking up the results of a previous run.
-The names of those results might include suffixes corresponding
-with the parse and assembly stage (cf. <b>--xo-dat</b> and
-<b>--xo-ass</b>).
-If you are not clear on this (and you should not be), exercise
-the <b>--whatif</b> option to be sure.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--start-format"></a><b>--start-format</b> (<i>skip earlier stages</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Immediately start the format stage.
-Assume the necessary files have been created in a previous run.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--help"></a><b>--help</b> (<i>summary of options</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Print a terse summary of options.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xi"></a><b>--xi</b> suf (<i>strip suffix from data file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-In normal usage, this will strip the specified suffix from the data file
-to obtain the base name for further output.
-When used with <b>--start-mcl</b>=<i>fname</i> the same behaviour is applied
-to the mcl input file name specified in <i>fname</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-dat"></a><b>--xo-dat</b> suf (<i>attach suf to parse output</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This suffix will be attached to the base name of the parse output.
-It can be used to distinguish between different parse parametrizations
-if this is applicable.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-ass"></a><b>--xo-ass</b> suf (<i>attach suf to assembly output</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This suffix will be attached to the base name of the assembly output.
-It can be used to distinguish between different assembly parametrizations
-if this is applicable.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-mcl"></a><b>--xo-mcl</b> suf (<i>replace mcl output suffix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This suffix will be used instead of the suffix by default created
-by the pipeline.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xa-mcl"></a><b>--xa-mcl</b> str (<i>append to mcl output suffix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This string will be appended to the suffix by default created
-by the pipeline.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xe-mcl"></a><b>--xe-mcl</b> suf (<i>append to mcl output</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This string will be appended as a single suffix to the output base
-name before mclpipeline appends its own suffix.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-fmt"></a><b>--xo-fmt</b> suf (<i>attach suf to clmformat output</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This suffix will be used instead of the suffix by default used
-by the formatting stage.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ass-repeat"></a><b>--ass-repeat</b> str (<i>assembly repeat option</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Corresponds with the <b>mcxassemble</b> <b>-r</b> <i>mode</i> option.
-Refer to the <a class="local sibling" href="mcxassemble.html">mcxassemble</a> manual.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ass-opt"></a><b>--ass-opt</b> val (<i>assembly option transporter</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transfer <b>-opt</b> <i>val</i> to <b>mcxassemble</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ass-nomap"></a><b>--ass-nomap</b> (<i>ignore map file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Either no map file is present or it should be ignored.
-For parsers that don't write map files.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-I"></a><b>--mcl-I</b> float (<i>mcl inflation value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The (main) inflation value mcl should use.
-<i>This is the primary mcl option</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-scheme"></a><b>--mcl-scheme</b> i (<i>mcl scheme index</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The scheme index to use. This options is also important.
-Refer to the <a class="local sibling" href="mcl.html">mcl</a> manual.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-te"></a><b>--mcl-te</b> num (<i>#expansion threads</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The number of threads <b>mcl</b> should use.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-i"></a><b>--mcl-i</b> float (<i>mcl initial inflation value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The initial inflation value mcl should use.
-Only for fine-tuning or testing.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-l"></a><b>--mcl-l</b> float (<i>mcl initial loop length</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The length of the loop in which initial inflation
-is applied. By default zero.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-c"></a><b>--mcl-c</b> float (<i>mcl center value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The center value. One may attempt to affect granularity
-by exercising this option, which controls the loop weights
-in the input matrix. Refer to the <a class="local sibling" href="mcl.html">mcl</a> manual.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-pi"></a><b>--mcl-pi</b> float (<i>mcl pre-inflation value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Pre-inflation, another option which may possibly affect granularity by
-changing the input matrix. It makes the edge weight
-distribution either more or less homogeneous.
-Refer to the <a class="local sibling" href="mcl.html">mcl</a> manual.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-o"></a><b>--mcl-o</b> fname (<i>do not use</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the mcl output name.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--mcl-opt"></a><b>--mcl-opt</b> val (<i>mcl option transporter</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transfer <b>-opt</b> <i>val</i> to <b>mcl</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-dump-stats"></a><b>--fmt-dump-stats</b> (<i>add simple measures to dump file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This adds some simple performance measures to the dump file. For each
-cluster, five columns proceed the label listing. These are the cluster ID,
-the number of elements in the cluster, the projection (percentage of
-within-cluster edge weight relative to total outgoing edge weight), the
-efficiency of the cluster (which is the average of the efficiency of all its
-nodes), and the maximum efficiency (average of the max-efficiency of all the
-nodes). Look into the <a class="local sibling" href="clmformat.html">clmformat manual</a> for more
-information on and references to the efficiency measures.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-fancy"></a><b>--fmt-fancy</b> (<i>create detailed output (requires zoem)</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Creates extensive description of node/cluster and cluster/cluster
-relationships.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-lump-count"></a><b>--fmt-lump-count</b> num (<i>collect formatted output</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Collect clusters in the same file until the total number
-of nodes has exceeded <i>num</i> (in the formatted output).
-Only meaninful when <b>--fmt-fancy</b> is given.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-tab"></a><b>--fmt-tab</b> (<i>use this tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Explicitly specify the tab file to use.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-notab"></a><b>--fmt-notab</b> (<i>ignore tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Either no tab file is present or it should be ignored.
-For parsers that don't write tab files.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-opt"></a><b>--fmt-opt</b> val (<i>clmformat option transporter</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transfer <b>-opt</b> <i>val</i> to <b>clm format</b>.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxdeblast.html">mcxdeblast</a>, <a class="local sibling" href="mclblastline.html">mclblastline</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-With default settings, <b>mclpipeline</b> depends on the presence
-of <b>zoem</b>. It can be obtained from
-<a class="extern" href="http://micans.org/zoem/">http://micans.org/zoem/</a> .
-</p>
-</body>
-</html>
diff --git a/doc/mclpipeline.ps b/doc/mclpipeline.ps
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diff --git a/doc/mcx.1 b/doc/mcx.1
deleted file mode 100644
index 05a326b..0000000
--- a/doc/mcx.1
+++ /dev/null
@@ -1,134 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx" 1 "16 May 2014" "mcx 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx \- perform various computations on graphs and matrices
-.SH SYNOPSIS
-
-.di ZV
-.in 0
-.nf \fC
- \fBmcx\fP <mode> [mode-options] [mode-files]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.SH DESCRIPTION
-
-\fBmcx\fP implements a variety of computations on graphs and matrices\&. The
-first argument to \fBmcx\fP should be a \fImode\fP, which is a string establishing
-the type of computation to invoke\&. Each mode \fImode\fP is described in the
-mcx\fImode\fP manual page\&. The currently available modes are
-\fBconvert\fP, \fBdiameter\fP, \fBclcf\fP, \fBq\fP and \fBctty\fP\&.
-The \fBconvert\fP mode is thus described in the
-\fBmcxconvert\fP manual page\&.
-
-Invoking \fBmcx\fP without arguments causes it to print out a list
-of available modes with a short description of the type of
-command line expected by that mode\&.
-
-Invoking \fBmcx\fP with just a mode will print out a longer listing
-of options available for that particular mode\&.
-Modes that are able to function normally without arguments
-can be invoked by adding the \fI--nop\fP argument\&.
-
-Several options are shared between all \fBmcx\fP modes\&. Note that
-these options are specified after the \fBmode\fP\&. See \fBOPTIONS\fP\&.
-
-The \fB--version\fP causes \fBmcx\fP to print out version
-and license information\&.
-
-Issuing \fImcx help mode\fP will cause \fBmcx\fP to look for a manual page
-describing \fImode\fP and display it if found\&. This requires that the
-MANPATH environment variable contains the directory in which the MCL-edge
-manual pages were installed\&. This will usually be \fCPREFIX/share\fP,
-where \fCPREFIX\fP is the path with which the software was configured\&.
-.SH OPTIONS
-
-These are options that pertain to all modes\&. They should be specified
-\fIafter\fP the mode argument\&.
-
-.ZI 2m "\fB-h\fP (\fIsynopsis\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--help\fP (\fIsynopsis\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-List available options\&.
-.in -2m
-
-.ZI 2m "\fB--nop\fP (\fIno-op\fP)"
-\&
-.br
-Not an option\&. This option has no effect then to increment
-the argument count\&. This can be useful for \fBmcx\fP modes which are able to
-function without any options\&. Such a mode typically reads from STDIN, writes
-to STDOUT, and uses default settings\&. However, simply specifying a mode
-without options leads \fBmcx\fP to output a list of available options for that
-mode\&. This can be prevented by using the \fB--nop\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-set\fP (\fIkey=val\fP)"
-\&
-.br
-Sets the key\ \&\fBkey\fP to value\ \&\fBval\fP in the environment\&.
-Some modes allow adjustment of settings in this manner\&.
-.in -2m
-
-.ZI 2m "\fB-progress\fP <num> (\fIprogress interval size\fP)"
-\&
-.br
-Defines the interval that defines the progress frequency\&.
-.in -2m
-
-.ZI 2m "\fB--debug\fP (\fIturn on debugging\fP)"
-\&
-.br
-Turn debugging on\&.
-.in -2m
-
-.ZI 2m "\fB--version\fP (\fIshow version\fP)"
-\&
-.br
-Show version\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcx.html b/doc/mcx.html
deleted file mode 100644
index 05f68fb..0000000
--- a/doc/mcx.html
+++ /dev/null
@@ -1,219 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
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-margin-right: 0%;
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-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
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-{ position: relative;
-margin-left: 8%;
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-body
-{ text-align: justify;
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-<title>The mcx manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcx.ps"><b>mcx</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx — perform various computations on graphs and matrices</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<div class="verbatim"> <b>mcx</b> <mode> [mode-options] [mode-files]</div>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx</b> implements a variety of computations on graphs and matrices. The
-first argument to <b>mcx</b> should be a <i>mode</i>, which is a string establishing
-the type of computation to invoke. Each mode <i>mode</i> is described in the
-mcx<i>mode</i> manual page. The currently available modes are
-<b>convert</b>, <b>diameter</b>, <b>clcf</b>, <b>q</b> and <b>ctty</b>.
-The <b>convert</b> mode is thus described in the
-<a class="local sibling" href="mcxconvert.html">mcxconvert</a> manual page.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Invoking <b>mcx</b> without arguments causes it to print out a list
-of available modes with a short description of the type of
-command line expected by that mode.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Invoking <b>mcx</b> with just a mode will print out a longer listing
-of options available for that particular mode.
-Modes that are able to function normally without arguments
-can be invoked by adding the <i>--nop</i> argument.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Several options are shared between all <b>mcx</b> modes. Note that
-these options are specified after the <b>mode</b>. See <a class="intern" href="#options">OPTIONS</a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--version</b> causes <b>mcx</b> to print out version
-and license information.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Issuing <i>mcx help mode</i> will cause <b>mcx</b> to look for a manual page
-describing <i>mode</i> and display it if found. This requires that the
-MANPATH environment variable contains the directory in which the MCL-edge
-manual pages were installed. This will usually be <tt>PREFIX/share</tt>,
-where <tt>PREFIX</tt> is the path with which the software was configured.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<p style="margin-bottom:0" class="asd_par">
-These are options that pertain to all modes. They should be specified
-<i>after</i> the mode argument.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade item_leftalign nowrap" ><a name="opt-h"></a><b>-h</b> (<i>synopsis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--help"></a><b>--help</b> (<i>synopsis</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-List available options.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--nop"></a><b>--nop</b> (<i>no-op</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Not an option. This option has no effect then to increment
-the argument count. This can be useful for <b>mcx</b> modes which are able to
-function without any options. Such a mode typically reads from STDIN, writes
-to STDOUT, and uses default settings. However, simply specifying a mode
-without options leads <b>mcx</b> to output a list of available options for that
-mode. This can be prevented by using the <b>--nop</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-set"></a><b>-set</b> (<i>key=val</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sets the key <b>key</b> to value <b>val</b> in the environment.
-Some modes allow adjustment of settings in this manner.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-progress"></a><b>-progress</b> <num> (<i>progress interval size</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Defines the interval that defines the progress frequency.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--debug"></a><b>--debug</b> (<i>turn on debugging</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Turn debugging on.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--version"></a><b>--version</b> (<i>show version</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Show version.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/mcxalter.1 b/doc/mcxalter.1
deleted file mode 100644
index 103caf7..0000000
--- a/doc/mcxalter.1
+++ /dev/null
@@ -1,112 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxalter" 1 "16 May 2014" "mcxalter 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxalter \- various network transformations
-.SH SYNOPSIS
-
-\fBmcxalter\fP
-\fB[-imx\fP <fname> (\fIspecify matrix/graph input\fP)\fB]\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[-icl\fP <fname> (\fIspecify cluster input\fP)\fB]\fP
-\fB[--block\fP (\fIuse within-cluster edges\fP)\fB]\fP
-\fB[--blockc\fP (\fIuse between-cluster edges\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-.SH DESCRIPTION
-
-This utility supplies various transformations of networks\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input that is in mcl native matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-With \fB-abc\fP this option will, additionally, construct
-a graph only on the labels found in the tab file\&.
-If this option is used in conjunction with \fB-imx\fP the
-tab domain and the matrix domain are required to be identical\&.
-.in -2m
-
-.ZI 2m "\fB-icl\fP <fname> (\fIspecify cluster input\fP)"
-\&
-.br
-Read in a cluster file for use with either \fB--block\fP or \fB--blockc\fP\&.
-.in -2m
-
-.ZI 2m "\fB--block\fP (\fIuse within-cluster edges\fP)"
-\&
-.br
-Remove between-cluster edges from the network\&. This is done first, before
-other transformations take effect\&.
-.in -2m
-
-.ZI 2m "\fB--blockc\fP (\fIuse between-cluster edges\fP)"
-\&
-.br
-Remove within-cluster edges from the network\&. This is done first, before
-other transformations take effect\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-.br
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
-\&
-.br
-Output file\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-\fBmcx(1)\fP,
-\fBmcxsubs(1)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxalter.html b/doc/mcxalter.html
deleted file mode 100644
index 1c2d79b..0000000
--- a/doc/mcxalter.html
+++ /dev/null
@@ -1,210 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
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-{ text-align: justify;
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-div.verbatim
-{ font-family: monospace;
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-{ margin-left: 8%;
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-{ position: relative;
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-<title>The mcxalter manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxalter.ps"><b>mcxalter</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxalter — various network transformations</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxalter</b>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix/graph input</i>)<b>]</b></a>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>specify cluster input</i>)<b>]</b></a>
-<a class="intern" href="#opt--block"><b>[--block</b> (<i>use within-cluster edges</i>)<b>]</b></a>
-<a class="intern" href="#opt--blockc"><b>[--blockc</b> (<i>use between-cluster edges</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-This utility supplies various transformations of networks.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in mcl native matrix format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-With <b>-abc</b> this option will, additionally, construct
-a graph only on the labels found in the tab file.
-If this option is used in conjunction with <b>-imx</b> the
-tab domain and the matrix domain are required to be identical.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>specify cluster input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read in a cluster file for use with either <b>--block</b> or <b>--blockc</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--block"></a><b>--block</b> (<i>use within-cluster edges</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Remove between-cluster edges from the network. This is done first, before
-other transformations take effect.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--blockc"></a><b>--blockc</b> (<i>use between-cluster edges</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Remove within-cluster edges from the network. This is done first, before
-other transformations take effect.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output file.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-<a class="local sibling" href="mcx.html">mcx</a>,
-<a class="local sibling" href="mcxsubs.html">mcxsubs</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/mcxarray.1 b/doc/mcxarray.1
deleted file mode 100644
index 4d2414d..0000000
--- a/doc/mcxarray.1
+++ /dev/null
@@ -1,495 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxarray" 1 "16 May 2014" "mcxarray 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxarray \- Transform array data to MCL matrices
-.SH SYNOPSIS
-
-\fBmcxarray\fP [options]
-
-\fBmcxarray\fP
-\fB[-data\fP fname (\fIinput data file\fP)\fB]\fP
-.br
-\fB[-imx\fP fname (\fIinput matrix file\fP)\fB]\fP
-.br
-\fB[-co\fP num (\fI(absolute) cutoff for output values (required)\fP)\fB]\fP
-.br
-\fB[-skipr\fP <num> (\fIskip <num> data rows\fP)\fB]\fP
-.br
-\fB[-skipc\fP <num> (\fIskip <num> data columns\fP)\fB]\fP
-.br
-\fB[-o\fP fname (\fIoutput file fname\fP)\fB]\fP
-.br
-\fB[--text-table\fP (\fIwrite output in full text table format\fP)\fB]\fP
-.br
-\fB[-write-tab\fP <fname> (\fIwrite row labels to file\fP)\fB]\fP
-.br
-\fB[-l\fP <num> (\fItake labels from column <num>\fP)\fB]\fP
-.br
-
-\fB[--pearson\fP (\fIuse Pearson correlation (default)\fP)\fB]\fP
-.br
-\fB[--spearman\fP (\fIuse Spearman rank correlation\fP)\fB]\fP
-.br
-\fB[--dot\fP (\fIuse dot product\fP)\fB]\fP
-.br
-\fB[--cosine\fP (\fIuse cosine (similarity)\fP)\fB]\fP
-.br
-\fB[--slow-cosine\fP (\fIuse cosine(0\&.5 alpha) (similarity)\fP)\fB]\fP
-
-\fB[--angle\fP (\fIuse angle between vectors (note: a metric distance)\fP)\fB]\fP
-.br
-\fB[--acute-angle\fP (\fIuse acute angle between vectors\fP)\fB]\fP
-.br
-\fB[--angle-norm\fP (\fIuse normalised angle between vectors (by pi)\fP)\fB]\fP
-.br
-\fB[--acute-angle-norm\fP (\fIuse normalised acute angle between vectors\ \&(by\ \&pi/2)\fP)\fB]\fP
-.br
-\fB[--sine\fP (\fIuse sine (note: a metric distance)\fP)\fB]\fP
-.br
-\fB[--slow-sine\fP (\fIuse sine(0\&.5 alpha) (note: a metric distance)\fP)\fB]\fP
-.br
-\fB[--euclid\fP (\fIuse Euclidean distance between vectors\fP)\fB]\fP
-.br
-\fB[--max\fP (\fIuse L-oo, aka Chebyshev distance\fP)\fB]\fP
-.br
-\fB[--taxi\fP (\fIuse L-1, aka taxi, aka city-block distance\fP)\fB]\fP
-.br
-\fB[-minkowski\fP <num> (\fIuse Minkowski distance with power <num>\fP)\fB]\fP
-.br
-\fB[-fp\fP <mode> (\fIuse fingerprint measure\fP)\fB]\fP
-.br
-
-\fB[-digits\fP <num> (\fIoutput precision\fP)\fB]\fP
-.br
-\fB[--write-binary\fP (\fIwrite output in binary format\fP)\fB]\fP
-.br
-\fB[-t\fP <int> (\fIuse <int> threads\fP)\fB]\fP
-.br
-\fB[-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)\fB]\fP
-.br
-\fB[-j\fP <intj> (\fIthis job has index <intj>\fP)\fB]\fP
-.br
-\fB[-start\fP <int> (\fIstart at column <int> inclusive\fP)\fB]\fP
-.br
-\fB[-end\fP <int> (\fIend at column <int> EXclusive\fP)\fB]\fP
-.br
-\fB[--transpose-data\fP (\fIwork with the transposed data matrix\fP)\fB]\fP
-.br
-\fB[--rank-transform\fP (\fIrank transform the data first\fP)\fB]\fP
-.br
-\fB[-tf\fP spec (\fItransform result network\fP)\fB]\fP
-.br
-\fB[-table-tf\fP spec (\fItransform input table before processing\fP)\fB]\fP
-.br
-\fB[-n\fP mode (\fInormalize input\fP)\fB]\fP
-.br
-\fB[--zero-as-na\fP (\fItreat zeroes as missing data\fP)\fB]\fP
-.br
-\fB[--sparse\fP (\fIdo not store zero values\fP)\fB]\fP
-.br
-\fB[-write-data\fP <fname> (\fIwrite data to file\fP)\fB]\fP
-.br
-\fB[-write-na\fP <fname> (\fIwrite NA matrix to file\fP)\fB]\fP
-.br
-\fB[--job-info\fP (\fIprint index ranges for this job\fP)\fB]\fP
-.br
-\fB[--help\fP (\fIprint this help\fP)\fB]\fP
-.br
-\fB[-h\fP (\fIprint this help\fP)\fB]\fP
-.br
-\fB[--version\fP (\fIprint version information\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcxarray\fP can either read a flat file containing array data (\fB-data\fP)
-or a matrix file satisfying the mcl input format (\fB-imx\fP)\&. In the
-former case it will by default work with the rows as the data vectors\&. In
-the latter case it will by default work with the columns as the data
-vectors (note that mcl matrices are presented as a listing of columns)\&.
-This can be changed for both using the
-\fB--transpose-data\fP option\&.
-
-The input data may contain missing data in the form of empty columns,
-NA values (not available/applicable), or NaN values (not a number)\&.
-The program keeps track of these, and when computing the correlation
-between two rows or columns ignores all positions where any one of
-the two has missing data\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-data\fP fname (\fIinput data file\fP)"
-\&
-.br
-Specify the data file containing the expression values\&.
-It should be tab-separated\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP fname (\fIinput matrix file\fP)"
-\&
-.br
-The expression values are read from a file in mcl matrix format\&.
-.in -2m
-
-.ZI 2m "\fB--pearson\fP (\fIuse Pearson correlation (default)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--spearman\fP (\fIuse Spearman rank correlation\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--cosine\fP (\fIuse cosine\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--slow-cosine\fP (\fIuse cosine(0\&.5 alpha) (similarity)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dot\fP (\fIuse the dot product\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-All these measures express the level of similarity or correlation
-between two vectors\&.
-Note that the dot product is not normalised and should only be used with
-very good reason\&. A few more similarity measures are provided by
-the fingerprint option \fB-fp\fP described below\&.
-.in -2m
-
-.ZI 2m "\fB-fp\fP <mode> (\fIspecify fingerprint measure\fP)"
-\&
-.br
-Fingerprints are used to define an entity in terms of it having
-or not having certain traits\&. This means that a fingerprint can be
-represented by a boolean vector, and a set of fingerprints can be represented
-by an array of such vectors\&. In the presence of many traits and entities the dimensions
-of such a matrix can grow large\&. The sparse storage employed by MCL-edge is
-ideally suited to this, and mcxarray is ideally suited to the computation
-of all pairwise comparisons between such fingerprints\&.
-Currently mcxarray supports five different types of fingerprint, described below\&.
-Given two fingerprints, the number of traits unique to the first is denoted by \fIa\fP,
-the number unique to the second is denoted by \fIb\fP, and the number that they
-have in common is denoted by \fIc\fP\&.
-
-.ZI 2m "hamming"
-\&
-.br
-The Hamming distance, defined as \fIa\fP+\fIb\fP\&.
-.in -2m
-
-.ZI 2m "tanimoto"
-\&
-.br
-The Tanimoto similarity measure, \fIc\fP/(\fIa\fP+\fIb\fP+\fIc\fP)\&.
-.in -2m
-
-.ZI 2m "cosine"
-\&
-.br
-The cosine similarity measure, \fIc\fP/sqrt((\fIa\fP+\fIc\fP)*(\fIb\fP+\fIc\fP))\&.
-.in -2m
-
-.ZI 2m "meet"
-\&
-.br
-Simply the number of shared traits, identical to \fIc\fP\&.
-.in -2m
-
-.ZI 2m "cover"
-\&
-.br
-A normalised and non-symmetric similarity measure, representing the fraction
-of traits shared relative to the number of traits by a single entity\&.
-This gives the value \fIc\fP/(\fIa\fP+\fIc\fP) in one direction, and the value
-\fIc\fP/(\fIb\fP+\fIc\fP) in the other\&.
-.in -2m
-.in -2m
-
-.ZI 2m "\fB--sine\fP (\fIuse sine (note: a metric distance)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--slow-sine\fP (\fIuse sine(0\&.5 alpha) (note: a metric distance)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--angle\fP (\fIuse angle between vectors (note: a metric distance)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--acute-angle\fP (\fIuse acute angle between vectors\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--angle-norm\fP (\fIuse normalised angle between vectors (by pi)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--acute-angle-norm\fP (\fIuse normalised acute angle between vectors (by pi/2)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--euclid\fP (\fIuse Euclidean distance between vectors\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--max\fP (\fIuse L-oo, aka Chebyshev distance\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--taxi\fP (\fIuse L-1, aka taxi, aka city-block, aka Manhattan distance\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-minkowski\fP <num> (\fIuse Minkowski distance with power <num>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-All these measures express the level of dissimilarity or distance
-between two vectors\&.
-.in -2m
-
-.ZI 2m "\fB-skipr\fP <num> (\fIskip <num> data rows\fP)"
-\&
-.br
-Skip the first \fI<num>\fP data rows\&.
-.in -2m
-
-.ZI 2m "\fB-skipc\fP <num> (\fIskip <num> data columns\fP)"
-\&
-.br
-Ignore the first \fI<num>\fP data columns\&.
-.in -2m
-
-.ZI 2m "\fB-l\fP <num> (\fItake labels from column <num>\fP)"
-\&
-.br
-Specifies to construct a tab of labels from this data column\&.
-The tab can be written to file using \fB-write-tab\fP\ \&\fIfname\fP\&.
-.in -2m
-
-.ZI 2m "\fB-write-tab\fP <fname> (\fIwrite row labels to file\fP)"
-\&
-.br
-Write a tab file\&. In the simple case where the labels are in the first
-data column it is sufficient to issue \fB-skipc\fP\ \&\fB1\fP\&.
-If more data columns need to be skipped one must explicitly specify
-the data column to take labels from with \fB-l\fP\ \&\fIl\fP\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <int> (\fIuse <int> threads\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-j\fP <intj> (\fIthis job has index <intj>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Computing all pairwise correlations is time-intensive for large input\&.
-If you have multiple CPUs available consider using as
-many threads\&. Additionally it is possible to spread the computation over
-multiple jobs/machines\&.
-These three options are described in the \fBclmprotocols\fP manual page\&.
-The following set of options, if given to as many commands, defines three jobs, each running four threads\&.
-
-.di ZV
-.in 0
-.nf \fC
--t 4 -J 3 -j 0 -o out\&.0
--t 4 -J 3 -j 1 -o out\&.1
--t 4 -J 3 -j 2 -o out\&.2
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The output can then be collected with
-
-.di ZV
-.in 0
-.nf \fC
-mcx collect --add-matrix -o out\&.all out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-
-.ZI 2m "\fB--job-info\fP (\fIprint index ranges for this job\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-start\fP <int> (\fIstart at column <int> inclusive\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-end\fP <int> (\fIend at column <int> EXclusive\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-\fB--job-info\fP can be used to list the set of column
-ranges to be processed by the job as a result of the command
-line options \fB-t\fP, \fB-J\fP, and \fB-j\fP\&.
-If a job has failed, this option can be used to manually
-split those ranges into finer chunks, each to be processed
-as a new sub-job specified with \fB-start\fP and \fB-end\fP\&.
-With the latter two options, it is impossible to use
-parallelization of any kind
-(i\&.e\&. any of the \fB-t\fP, \fB-J\fP, and \fB-j\fP options)\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file fname\fP)"
-\&
-.br
-Output file name\&.
-.in -2m
-
-.ZI 2m "\fB--text-table\fP (\fIwrite output in full text table format\fP)"
-\&
-.br
-The output will be written in tabular format rather than native \fBmcl-edge\fP format\&.
-.in -2m
-
-.ZI 2m "\fB-digits\fP <num> (\fIoutput precision\fP)"
-\&
-.br
-Specify the precision to use in native interchange format\&.
-.in -2m
-
-.ZI 2m "\fB--write-binary\fP (\fIwrite output in binary format\fP)"
-\&
-.br
-Write output matrices in native binary format\&.
-.in -2m
-
-.ZI 2m "\fB-co\fP num (\fI(absolute) cutoff for output values\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Output values of magnitude smaller than \fInum\fP are removed (set to zero)\&.
-Thus, negative values are removed only if their positive counterpart
-is smaller than \fInum\fP\&.
-.in -2m
-
-.ZI 2m "\fB--transpose-data\fP (\fIwork with the transpose\fP)"
-\&
-.br
-Work with the transpose of the input data matrix\&.
-.in -2m
-
-.ZI 2m "\fB--rank-transform\fP (\fIrank transform the data first\fP)"
-\&
-.br
-The data is rank-transformed prior to the computation of pairwise measures\&.
-.in -2m
-
-.ZI 2m "\fB-write-data\fP <fname> (\fIwrite data to file\fP)"
-\&
-.br
-This writes the data that was read in to file\&.
-If \fB--spearman\fP is specified the data will
-be rank-transformed\&.
-.in -2m
-
-.ZI 2m "\fB-write-na\fP <fname> (\fIwrite NA matrix to file\fP)"
-\&
-.br
-This writes all positions for which no data was found
-to file, in native mcl matrix format\&.
-.in -2m
-
-.ZI 2m "\fB--zero-as-na\fP (\fItreat zeroes as missing data\fP)"
-\&
-.br
-This option can be useful when reading data with the \fB-imx\fP option,
-for example after it has been loaded from label input by \fBmcxload\fP\&.
-An example case is the processing of a large number of probe rankings,
-where not all rankings contain all probe names\&. The rankings can be loaded
-using \fBmcxload\fP with a tab file containing all probe names\&.
-Probes that are present in the ranking are given a positive ordinal
-number reflecting the ranking, and probes that are absent are implicitly
-given the value zero\&. With the present option mcxarray will handle
-the correlation computation in a reasonable way\&.
-.in -2m
-
-.ZI 2m "\fB--sparse\fP (\fIdo not store zero data value\fP)"
-\&
-.br
-With this option internal calculations are performed on compressed
-data where zeroes are not stored\&. This can be useful when the input
-data is very large\&.
-.in -2m
-
-.ZI 2m "\fB-n\fP mode (\fInormalization mode\fP)"
-\&
-.br
-If \fImode\fP is set to \fBz\fP the data will be normalized
-based on z-score\&. No other modes are currently supported\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP spec (\fItransform result network\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-table-tf\fP spec (\fItransform input table before processing\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The transformation syntax is described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB--help\fP (\fIprint help\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-h\fP (\fIprint help\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB--version\fP (\fIprint version information\fP)"
-\&
-.br
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcl(1)\fP,
-\fBmclfaq(7)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxarray.html b/doc/mcxarray.html
deleted file mode 100644
index 9b2aae3..0000000
--- a/doc/mcxarray.html
+++ /dev/null
@@ -1,437 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-{ font-family: monospace;
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-body
-{ text-align: justify;
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-}
-</style>
-<title>The mcxarray manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxarray.ps"><b>mcxarray</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxarray — Transform array data to MCL matrices</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxarray</b> [options]</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxarray</b>
-<a class="intern" href="#opt-data"><b>[-data</b> fname (<i>input data file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-imx"><b>[-imx</b> fname (<i>input matrix file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-co"><b>[-co</b> num (<i>(absolute) cutoff for output values (required)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-skipr"><b>[-skipr</b> <num> (<i>skip <num> data rows</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-skipc"><b>[-skipc</b> <num> (<i>skip <num> data columns</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file fname</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--text-table"><b>[--text-table</b> (<i>write output in full text table format</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-write-tab"><b>[-write-tab</b> <fname> (<i>write row labels to file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-l"><b>[-l</b> <num> (<i>take labels from column <num></i>)<b>]</b></a><br>
-
-<a class="intern" href="#opt--pearson"><b>[--pearson</b> (<i>use Pearson correlation (default)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--spearman"><b>[--spearman</b> (<i>use Spearman rank correlation</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--dot"><b>[--dot</b> (<i>use dot product</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--cosine"><b>[--cosine</b> (<i>use cosine (similarity)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--slow-cosine"><b>[--slow-cosine</b> (<i>use cosine(0.5 alpha) (similarity)</i>)<b>]</b></a>
-
-<a class="intern" href="#opt--angle"><b>[--angle</b> (<i>use angle between vectors (note: a metric distance)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--acute-angle"><b>[--acute-angle</b> (<i>use acute angle between vectors</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--angle-norm"><b>[--angle-norm</b> (<i>use normalised angle between vectors (by pi)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--acute-angle-norm"><b>[--acute-angle-norm</b> (<i>use normalised acute angle between vectors (by pi/2)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--sine"><b>[--sine</b> (<i>use sine (note: a metric distance)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--slow-sine"><b>[--slow-sine</b> (<i>use sine(0.5 alpha) (note: a metric distance)</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--euclid"><b>[--euclid</b> (<i>use Euclidean distance between vectors</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--max"><b>[--max</b> (<i>use L-oo, aka Chebyshev distance</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--taxi"><b>[--taxi</b> (<i>use L-1, aka taxi, aka city-block distance</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-minkowski"><b>[-minkowski</b> <num> (<i>use Minkowski distance with power <num></i>)<b>]</b></a><br>
-<a class="intern" href="#opt-fp"><b>[-fp</b> <mode> (<i>use fingerprint measure</i>)<b>]</b></a><br>
-
-<a class="intern" href="#opt-digits"><b>[-digits</b> <num> (<i>output precision</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>write output in binary format</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-t"><b>[-t</b> <int> (<i>use <int> threads</i>)<b>]</b></a>
-<br>
-<a class="intern" href="#opt-J"><b>[-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)<b>]</b></a>
-<br>
-<a class="intern" href="#opt-j"><b>[-j</b> <intj> (<i>this job has index <intj></i>)<b>]</b></a>
-<br>
-<a class="intern" href="#opt-start"><b>[-start</b> <int> (<i>start at column <int> inclusive</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-end"><b>[-end</b> <int> (<i>end at column <int> EXclusive</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--transpose-data"><b>[--transpose-data</b> (<i>work with the transposed data matrix</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--rank-transform"><b>[--rank-transform</b> (<i>rank transform the data first</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>transform result network</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-table-tf"><b>[-table-tf</b> spec (<i>transform input table before processing</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-n"><b>[-n</b> mode (<i>normalize input</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--zero-as-na"><b>[--zero-as-na</b> (<i>treat zeroes as missing data</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--sparse"><b>[--sparse</b> (<i>do not store zero values</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-write-data"><b>[-write-data</b> <fname> (<i>write data to file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-write-na"><b>[-write-na</b> <fname> (<i>write NA matrix to file</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--job-info"><b>[--job-info</b> (<i>print index ranges for this job</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--help"><b>[--help</b> (<i>print this help</i>)<b>]</b></a><br>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print this help</i>)<b>]</b></a><br>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version information</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxarray</b> can either read a flat file containing array data (<b>-data</b>)
-or a matrix file satisfying the mcl input format (<b>-imx</b>). In the
-former case it will by default work with the rows as the data vectors. In
-the latter case it will by default work with the columns as the data
-vectors (note that mcl matrices are presented as a listing of columns).
-This can be changed for both using the
-<a class="intern" href="#opt--transpose-data"><b>--transpose-data</b> option</a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The input data may contain missing data in the form of empty columns,
-NA values (not available/applicable), or NaN values (not a number).
-The program keeps track of these, and when computing the correlation
-between two rows or columns ignores all positions where any one of
-the two has missing data.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-data"></a><b>-data</b> fname (<i>input data file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the data file containing the expression values.
-It should be tab-separated.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input matrix file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The expression values are read from a file in mcl matrix format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--pearson"></a><b>--pearson</b> (<i>use Pearson correlation (default)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--spearman"></a><b>--spearman</b> (<i>use Spearman rank correlation</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--cosine"></a><b>--cosine</b> (<i>use cosine</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-All these measures express the level of similarity or correlation
-between two vectors.
-Note that the dot product is not normalised and should only be used with
-very good reason. A few more similarity measures are provided by
-the fingerprint option <b>-fp</b> described below.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-fp"></a><b>-fp</b> <mode> (<i>specify fingerprint measure</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">Fingerprints are used to define an entity in terms of it having
-or not having certain traits. This means that a fingerprint can be
-represented by a boolean vector, and a set of fingerprints can be represented
-by an array of such vectors. In the presence of many traits and entities the dimensions
-of such a matrix can grow large. The sparse storage employed by <span class="smallcaps">MCL</span>-edge is
-ideally suited to this, and mcxarray is ideally suited to the computation
-of all pairwise comparisons between such fingerprints.
-Currently mcxarray supports five different types of fingerprint, described below.
-Given two fingerprints, the number of traits unique to the first is denoted by <i>a</i>,
-the number unique to the second is denoted by <i>b</i>, and the number that they
-have in common is denoted by <i>c</i>.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " >hamming</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">The Hamming distance, defined as <i>a</i>+<i>b</i>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >tanimoto</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">The Tanimoto similarity measure, <i>c</i>/(<i>a</i>+<i>b</i>+<i>c</i>).</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >cosine</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">The cosine similarity measure, <i>c</i>/sqrt((<i>a</i>+<i>c</i>)*(<i>b</i>+<i>c</i>)).</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >meet</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">Simply the number of shared traits, identical to <i>c</i>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >cover</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">A normalised and non-symmetric similarity measure, representing the fraction
-of traits shared relative to the number of traits by a single entity.
-This gives the value <i>c</i>/(<i>a</i>+<i>c</i>) in one direction, and the value
-<i>c</i>/(<i>b</i>+<i>c</i>) in the other.
-</p>
-</div>
-</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--sine"></a><b>--sine</b> (<i>use sine (note: a metric distance)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--slow-sine"></a><b>--slow-sine</b> (<i>use sine(0.5 alpha) (note: a metric distance)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--angle"></a><b>--angle</b> (<i>use angle between vectors (note: a metric distance)</i>)</div>< [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-All these measures express the level of dissimilarity or distance
-between two vectors.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-skipr"></a><b>-skipr</b> <num> (<i>skip <num> data rows</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Skip the first <i><num></i> data rows.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-skipc"></a><b>-skipc</b> <num> (<i>skip <num> data columns</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Ignore the first <i><num></i> data columns.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-l"></a><b>-l</b> <num> (<i>take labels from column <num></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specifies to construct a tab of labels from this data column.
-The tab can be written to file using <a class="intern" href="#opt-write-tab"><b>-write-tab</b> <i>fname</i></a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-tab"></a><b>-write-tab</b> <fname> (<i>write row labels to file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write a tab file. In the simple case where the labels are in the first
-data column it is sufficient to issue <b>-skipc</b> <b>1</b>.
-If more data columns need to be skipped one must explicitly specify
-the data column to take labels from with <b>-l</b> <i>l</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-t"></a><b>-t</b> <int> (<i>use <int> threads</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-J"></a><b>-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-j"></a><b>-j</b> <intj> (<i>this job has index <intj></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Computing all pairwise correlations is time-intensive for large input.
-If you have multiple CPUs available consider using as
-many threads. Additionally it is possible to spread the computation over
-multiple jobs/machines.
-These three options are described in the <a class="local sibling" href="clmprotocols.html">clmprotocols</a> manual page.
-The following set of options, if given to as many commands, defines three jobs, each running four threads.
-</p>
-<div class="verbatim">-t 4 -J 3 -j 0 -o out.0
--t 4 -J 3 -j 1 -o out.1
--t 4 -J 3 -j 2 -o out.2</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output can then be collected with
-</p>
-<div class="verbatim">mcx collect --add-matrix -o out.all out.[0-2]</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--job-info"></a><b>--job-info</b> (<i>print index ranges for this job</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-start"></a><b>-start</b> <int> (<i>start at column <int> inclusive</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-end"></a><b>-end</b> <int> (<i>end at column <int> EXclusive</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>--job-info</b> can be used to list the set of column
-ranges to be processed by the job as a result of the command
-line options <b>-t</b>, <b>-J</b>, and <b>-j</b>.
-If a job has failed, this option can be used to manually
-split those ranges into finer chunks, each to be processed
-as a new sub-job specified with <b>-start</b> and <b>-end</b>.
-With the latter two options, it is impossible to use
-parallelization of any kind
-(i.e. any of the <b>-t</b>, <b>-J</b>, and <b>-j</b> options).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file fname</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output file name.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--text-table"></a><b>--text-table</b> (<i>write output in full text table format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The output will be written in tabular format rather than native <b>mcl-edge</b> format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-digits"></a><b>-digits</b> <num> (<i>output precision</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the precision to use in native interchange format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--write-binary"></a><b>--write-binary</b> (<i>write output in binary format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write output matrices in native binary format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-co"></a><b>-co</b> num (<i>(absolute) cutoff for output values</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output values of magnitude smaller than <i>num</i> are removed (set to zero).
-Thus, negative values are removed only if their positive counterpart
-is smaller than <i>num</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--transpose-data"></a><b>--transpose-data</b> (<i>work with the transpose</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Work with the transpose of the input data matrix.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rank-transform"></a><b>--rank-transform</b> (<i>rank transform the data first</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The data is rank-transformed prior to the computation of pairwise measures.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-data"></a><b>-write-data</b> <fname> (<i>write data to file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This writes the data that was read in to file.
-If <b>--spearman</b> is specified the data will
-be rank-transformed.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-na"></a><b>-write-na</b> <fname> (<i>write NA matrix to file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This writes all positions for which no data was found
-to file, in native mcl matrix format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--zero-as-na"></a><b>--zero-as-na</b> (<i>treat zeroes as missing data</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option can be useful when reading data with the <b>-imx</b> option,
-for example after it has been loaded from label input by <a class="local sibling" href="mcxload.html">mcxload</a>.
-An example case is the processing of a large number of probe rankings,
-where not all rankings contain all probe names. The rankings can be loaded
-using <a class="local sibling" href="mcxload.html">mcxload</a> with a tab file containing all probe names.
-Probes that are present in the ranking are given a positive ordinal
-number reflecting the ranking, and probes that are absent are implicitly
-given the value zero. With the present option mcxarray will handle
-the correlation computation in a reasonable way.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--sparse"></a><b>--sparse</b> (<i>do not store zero data value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-With this option internal calculations are performed on compressed
-data where zeroes are not stored. This can be useful when the input
-data is very large.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-n"></a><b>-n</b> mode (<i>normalization mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If <i>mode</i> is set to <b>z</b> the data will be normalized
-based on z-score. No other modes are currently supported.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-tf"></a><b>-tf</b> spec (<i>transform result network</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-table-tf"></a><b>-table-tf</b> spec (<i>transform input table before processing</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The transformation syntax is described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--help"></a><b>--help</b> (<i>print help</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-h"></a><b>-h</b> (<i>print help</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--version"></a><b>--version</b> (<i>print version information</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcl.html">mcl</a>,
-<a class="local sibling" href="mclfaq.html">mclfaq</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/mcxassemble.1 b/doc/mcxassemble.1
deleted file mode 100644
index de89b43..0000000
--- a/doc/mcxassemble.1
+++ /dev/null
@@ -1,560 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxassemble" 1 "16 May 2014" "mcxassemble 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxassemble \- transform raw cooccurrence data to mcl matrix format\&.
-.SH SYNOPSIS
-
-\fBmcxassemble\fP
-\fB-b\fP base (\fIbase name\fP)
-\fB[-o\fP fname (\fIwrite to file fname\fP)\fB]\fP
-\fB[--write-binary\fP (\fIwrite output in binary format\fP)\fB]\fP
-\fB[--map\fP (\fIapply base\&.map\fP)\fB]\fP
-\fB[-raw-tf\fP (\fIapply transform spec to input\fP)\fB]\fP
-\fB[-rv\fP MODE (\fIrepeated vectors\fP)\fB]\fP
-\fB[-re\fP MODE (\fIrepeated entries\fP)\fB]\fP
-\fB[-ri\fP MODE (\fIadding mirror image\fP)\fB]\fP
-\fB[-r\fP MODE (\fIrepeated entries/vectors/images\fP)\fB]\fP
-\fB[-prm-tf\fP (\fIapply transform spec to primary matrix\fP)\fB]\fP
-\fB[-sym-tf\fP (\fIapply transform spec to symmetrified matrix\fP)\fB]\fP
-\fB[-q\fP (\fIquiet mode\fP)\fB]\fP
-
-The options above embody the default setup when using mcxassemble\&.
-There are many more options which mostly provide subtly different
-ways of doing input/output, set warning levels, or regulate
-how repeated entries and vectors should be treated\&.
-The full list of options is shown below\&.
-Read \fBDESCRIPTION\fP for learning about mcxassemble input/output
-and the functionality it provides\&.
-
-\fBNOTE\fP
-.br
-As of release 05-314 \fBmcl(1)\fP is able to cluster label-type input
-on the fly\&. In most cases, this will be sufficient\&. Alternatively,
-\fBmcxload(1)\fP can be used to map label-type input onto mcl
-matrices\&. Consequently, there are likely fewer scenarios nowadays
-where \fBmcxassemble\fP is the best solution\&. Consider first whether
-\fBmcl\fP in label mode or \fBmcxload\fP can do the job as well\&.
-
-\fBmcxassemble\fP
-\fB[-b\fP base (\fIbase name\fP)\fB]\fP
-\fB[-hdr\fP fname (\fIread header file\fP)\fB]\fP
-\fB[-raw\fP fname (\fIread raw file\fP)\fB]\fP
-\fB[--map\fP (\fIapply base\&.map\fP)\fB]\fP
-\fB[--cmap\fP (\fIapply base\&.cmap\fP)\fB]\fP
-\fB[--rmap\fP (\fIapply base\&.rmap\fP)\fB]\fP
-\fB[-map\fP fname (\fIapply fname\fP)\fB]\fP
-\fB[-rmap\fP fname (\fIapply fname\fP)\fB]\fP
-\fB[-cmap\fP fname (\fIapply fname\fP)\fB]\fP
-\fB[-tag\fP tag (\fIapply base\&.tag\fP)\fB]\fP
-\fB[-rtag\fP tag (\fIapply base\&.tag\fP)\fB]\fP
-\fB[-ctag\fP tag (\fIapply base\&.tag\fP)\fB]\fP
-\fB[-skw\fP fname (\fIwrite skew matrix\fP)\fB]\fP
-\fB[-prm\fP fname (\fIwrite primary result matrix\fP)\fB]\fP
-\fB[--skw\fP (\fIwrite base\&.skw\fP)\fB]\fP
-\fB[--prm\fP (\fIwrite base\&.prm\fP)\fB]\fP
-\fB[-xo\fP suf (\fIwrite base\&.suf\fP)\fB]\fP
-\fB[-o\fP fname (\fIwrite to file fname\fP)\fB]\fP
-\fB[-n\fP (\fIdo not write default symmetrized result\fP)\fB]\fP
-\fB[-i\fP (\fIread from single data file\fP)\fB]\fP
-\fB[-digits\fP int (\fIdigits width\fP)\fB]\fP
-\fB[-s\fP (\fIcheck for symmetry\fP)\fB]\fP
-\fB[-raw-tf\fP (\fIapply transform spec to input\fP)\fB]\fP
-\fB[-rv\fP <mode> (\fIaction for repeated vectors\fP)\fB]\fP
-\fB[-re\fP <mode> (\fIaction for repeated entries\fP)\fB]\fP
-\fB[-ri\fP <mode> (\fIadding mirror image\fP)\fB]\fP
-\fB[-r\fP <mode> (\fIsame for entries and vectors\fP)\fB]\fP
-\fB[-prm-tf\fP (\fIapply transform spec to primary matrix\fP)\fB]\fP
-\fB[-sym-tf\fP (\fIapply transform spec to symmetrified matrix\fP)\fB]\fP
-\fB[--quiet-re\fP (\fIquiet for repeated entries\fP)\fB]\fP
-\fB[--quiet-rv\fP (\fIquiet for repeated vectors\fP)\fB]\fP
-\fB[-q\fP (\fIthe two above combined\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcxassemble\fP enables easy matrix creation from an intermediate raw matrix
-format that can easily be constructed from a one-pass-parse of cooccurrence
-data\&. The basic setup is as follows\&.
-
-.ZJ 1m 1m "\(bu"
-Parse cooccurrence data from some external format\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Transform cooccurrence data to raw mcl data as you parse\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-When done, write out required header and domain information
-to a separate file\&. The domain information can be built during
-the parsing stage\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Use mcxassemble to construct a valid matrix from the raw data
-and the header information\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Nodes can optionally be relabeled by writing a separate map file to be read
-by \fBmcxassemble\fP, which takes the form of a very thin matrix file\&.
-.in -2m
-
-The easiest thing to do is to group all input/output files under the same
-base name, say\ \&\fBbase\fP\&. A standard way of proceeding, which will lead to
-a concise \fBmcxassemble\fP command line, is by creating the input files
-\fBbase\&.raw\fP and \fBbase\&.hdr\fP, and optionally the file \fBbase\&.map\fP\&. The
-default behaviour of mcxassemble is then to create \fBbase\&.sym\fP as the
-resulting matrix file, containing the symmetrized matrix constructed from
-the raw input\&.
-
-\fBExample\fP
-.br
-Suppose \fCblastresult\fP is a file containing blast results\&.
-The following two commands construct an mcl matrix file from the file\&.
-
-.di ZV
-.in 0
-.nf \fC
- mcxdeblast --score=e --sort=a blastresult
- mcxassemble -b blastresult -r max --map
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-\fBmcxdeblast\fP will generate the
-files \fCblastresult\&.hdr\fP, \fCblastresult\&.raw\fP, and \fCblastresult\&.map\fP\&.
-The \fB--sort=a\fP option will create a map file corresponding
-with alphabetic ordering\&. These files are processed by \fBmcxassemble\fP
-and it will generate the file \fCblastresult\&.sym\fP\&. The \fB-r\fP
-option tells \fBmcxassemble\fP that repeated entries should be maxed;
-each time the largest entry seen thus far will be taken\&.
-
-\fBHeader file\fP
-.br
-This file contains a header as usually found in generic mcl matrix files,
-i\&.e\&. the required \fIheader\fP part, and optionally the \fIdomain\fP part(s)
-if not all domains are canonical\&. Refer to \fBmcxio(5)\fP for more information\&.
-The domain information in the header file will be used to pre-construct a
-skeleton matrix and to validate the entries in the raw data file as they
-fill the skeleton matrix\&.
-
-\fBRaw input format\fP
-.br
-The file from which raw input is read should have the raw format as
-described in \fBmcxio(5)\fP\&. Simply put; no header specification, no domain
-specification, and no matrix introduction syntax is used\&. The file just
-contains a listing of vectors\&. An example fragment is the following:
-
-.nf \fC
-2 4:0\&.34 1:2\&.8838 4:2\&.328 1:4\&.238 1:12 $
-1 2:7\&.8 $
-2 1:0\&.01 4:20\&.3 3:2 $
-.fi \fR
-
-The listing of vectors need not be sorted, and neither does
-a vector itself need to be sorted - the mcl generic matrix format
-is actually not different in this respect\&.
-Furthermore, duplicate entries and duplicate vectors are allowed\&.
-This is in fact again allowed in the generic format, except
-that where applications expect generic format warnings will be issued and
-duplicate entries will be disregarded\&. \fBmcxassemble\fP allows customizable
-behaviour dictating how to merge repeated entries\&.
-Refer to the \fB-re\fP,\ \&\fB-rv\fP,\ \&\fB-r\fP
-options below\&.
-
-The vectors read by \fBmcxassemble\fP do have to match the domains specified in
-the header file\&. The leading index that specifies the column index has to be
-present in the column domain; all subsequent indices that specify column
-entries have to be present in the row domain\&.
-
-\fIIf one concatenates the contents of the header file and the data file\fP,
-the result is \fIalmost but not quite\fP a file containing a matrix in
-syntactically correct mcl generic matrix format\&. The parts missing
-are the \fC(mclmatrix\fP introduction token, (followed by) the
-\fCbegin\fP token, and the closing \fC)\fP token\&.
-
-\fBMap file\fP
-.br
-This file must contain a map matrix, which is a matrix with the
-following properties:
-
-.ZJ 1m 1m "\(bu"
-The column domain and row domain are of the same cardinality\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Each column has exactly one entry\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Each row domain index occurs in exactly one column\&.
-.in -2m
-
-Such a matrix is used to relabel the nodes as found in the raw data\&. A
-situation that might occur when parsing some external format (and producing
-raw matrix format), is that ID\&'s (indices) are handed out on the fly during
-the parse\&. Afterwards, one may want to relabel the IDs such that they
-correspond with an alphabetic listing of the quantity that is represented by
-the node domain, or by some other sort criterion\&. A map file is then
-typically generated by the parser, as that is the utility in charge of the
-IDs\&. A small example of a map file for a graph containing five nodes is the
-following:
-
-.di ZV
-.in 0
-.nf \fC
-(mclheader
-mcltype matrix
-dimensions 5x5
-)
-(mclmatrix
-begin
-0 4 $ # mno
-1 2 $ # ghi
-2 1 $ # def
-3 3 $ # jkl
-4 0 $ # abc
-)
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This corresponds to a relabeling such that the associated strings
-will be ordered alphabetically\&. Note that comments can be used
-to link string identifiers with indices\&. This map file says e\&.g\&. that
-the string identifier "mno" is represented by index 0 in the raw data,
-and by index 4 in the matrix output by \fBmcxassemble\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-b\fP base (\fIbase name\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Base name of files to be processed and output\&. Refer to \fBDESCRIPTION\fP
-above and the entries of other options below\&.
-.in -2m
-
-.ZI 2m "\fB-hdr\fP fname (\fIread header file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-raw\fP fname (\fIread raw file\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Explicitly specify the header file and the data file (rather
-than constructing the file names from a base name and suffixes)\&.
-.in -2m
-
-.ZI 2m "\fB--map\fP (\fIapply base\&.map\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--cmap\fP (\fIapply base\&.cmap\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--rmap\fP (\fIapply base\&.rmap\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-map\fP fname (\fIapply fname\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-rmap\fP fname (\fIapply fname\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cmap\fP fname (\fIapply fname\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-tag\fP tag (\fIapply base\&.tag\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-rtag\fP tag (\fIapply base\&.tag\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ctag\fP tag (\fIapply base\&.tag\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Map options\&. \fB--cmap\fP combines with the \fB-b\fP\ \&option,
-and says that the map file in \fBbase\fP\&.\fCcmap\fP (where \fBbase\fP
-was specified with \fB-b\fP\ \&\fBbase\fP) should be applied to the column
-domain only\&. \fB--rmap\fP works the same for the
-row domain, and \fB--map\fP can be used to apply the same map
-to both the column and row domains\&.
-
-\fB-cmap\fP and its siblings are used to explicitly specify the
-map file to be used, rather than combining a base name with a fixed
-suffix\&.
-\fB-tag\fP and its siblings work in conjuction with
-the \fB-b\fP\ \&option, and require that a tag be specified from
-which to construct the map file (by appending it to the base name)\&.
-.in -2m
-
-.ZI 2m "\fB-skw\fP fname (\fIwrite skew matrix\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-prm\fP fname (\fIwrite primary result matrix\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--prm\fP (\fIwrite base\&.prm\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--skw\fP (\fIwrite base\&.skw\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-n\fP (\fIdo not write default symmetrized result\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Options for writing matrices other than the default symmetrized result\&.
-The primary result matrix is the matrix constructed from reading in the
-raw data and adding entries to the skeleton matrix as specified
-with the \fB-r\fP, \fB-re\fP, and \fB-rv\fP options\&.
-This matrix can be written using one of the \fBprm\fP options\&.
-Calling the primary matrix A, the skew matrix (as defined here)
-is the matrix \fCA\ \&-\ \&A^T\fP, i\&.e\&. A minus its transposed matrix\&.
-It can be written using one of the \fBskw\fP options\&.
-
-If for some reason the symmetrized result is not needed, its output
-can be prevented using the \fB-n\fP\ \&option\&.
-.in -2m
-
-.ZI 2m "\fB-xo\fP suf (\fIwrite base\&.suf\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-o\fP fname (\fIwrite to file fname\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-i\fP (\fIread from single data file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-digits\fP int (\fIdigits width\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-binary\fP (\fIwrite output in binary format\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The \fB-xo\fP\ \&option is used in conjunction with the \fB-b\fP\ \&option
-in order to change the suffix for the file in which the symmetrized
-result matrix is written\&. Use e\&.g\&. \fB-xo\fP\ \&\fBmci\fP to change the suffix
-from the default value \fCsym\fP to \fCmci\fP\&. Use \fB-o\fP to explicitly
-specify the filename in full\&. Use \fB-digits\fP to set the number of
-digits written for matrix entries (c\&.q\&. edge weights)\&.
-
-The \fB-i\fP option is special\&. It causes
-\fBmcxassemble\fP to read both the header information and the raw data
-from the same file, where the syntax should be fully conforming
-to generic mcl matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-s\fP (\fIcheck for symmetry\fP)"
-\&
-.br
-This will check whether the primary result matrix was symmetric\&.
-It reports the number of failing (or \fIskew\fP) edges\&.
-.in -2m
-
-.ZI 2m "\fB-raw-tf\fP <tf-spec> (\fIapply transform spec to input\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-prm-tf\fP (\fIapply transform spec to primary matrix\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-sym-tf\fP (\fIapply transform spec to symmetrified matrix\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The first applies its transformation spec to the values
-as found in the raw data\&. The second applies its transformation
-spec to the primary matrix\&. The third applies its transformation
-step to the symmetrified matrix\&.
-Refer to \fBmcxio(5)\fP for documentation on the transformation
-spec syntax\&.
-.in -2m
-
-.ZI 2m "\fB-rv\fP add|max|min|mul|left|right (\fIaction for repeated vectors\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-re\fP add|max|min|mul|left|right (\fIaction for repeated entries\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-ri\fP add|max|min|mul (\fIadding mirror image\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-r\fP add|max|min|mul|left|right (\fIsame for entries and vectors\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Merge options, dictating the behaviour when repeated entries are
-found\&. A distinction is made between entries that are repeated within
-the same column listing, and entries that are repeated between
-different column listings\&. An entry can be a repeat of both kinds
-simultaneously as well\&.
-Additionally, the final result is by default symmetrized by combining with
-the mirror image (in matrix terminology, the \fItransposed\fP matrix)\&. This
-symmetrization can be done in the same variety of ways\&.
-
-The \fBre\fP option, for repeats within the same column, is carried out
-first\&. It is applied \fIafter\fP the column has its entries sorted, so the
-\fCleft\fP and \fCright\fP options are not garantueed to follow the order found
-in the raw input\&. The \fBrv\fP option, for repeats over different columns,
-is carried out second\&.
-
-The option \fB-ri\fP\ \&\fBmin\fP can assist in implementing
-a (top-list) best reciprocal hit criterion\&.
-
-\fBExamples\fP
-.br
-The column
-
-.di ZV
-.in 0
-.nf \fC
-0 1:30 1:50 2:60 4:70 3:20 1:40 2:40 $
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-is encountered in the input, listing entries for the vector labeled
-with index\ \&\fC0\fP\&. If \fB-re\fP\ \&\fBadd\fP or \fB-r\fP\ \&\fBadd\fP
-is used, it will transform to the vector
-
-.di ZV
-.in 0
-.nf \fC
-0 1:120 2:60 3:20 4:70 $
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-If \fB-re\fP\ \&\fBmax\fP or \fB-r\fP\ \&\fBadd\fP
-is used instead, it will transform to the vector
-
-.di ZV
-.in 0
-.nf \fC
-0 1:40 2:60 3:20 4:70 $
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Suppose \fIadd\fP mode is used, and that later on another
-vector specification for the index\ \&\fC0\fP is found, leading
-to this transformed vector:
-
-.di ZV
-.in 0
-.nf \fC
-0 1:60 2:80 4:40 $
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-If \fB-rv\fP\ \&\fBmax\fP was specified, this new vector is combined with the
-previous vector by taking the entry wise maximum:
-
-.di ZV
-.in 0
-.nf \fC
-0 1:120 2:60 3:20 4:70 $ # first (transformed) vector
-0 1:60 2:80 4:40 $ # second vector
-
-0 1:120 2:80 3:20 4:70 $ # entry wise maximum
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Finally, suppose that somewhere one or more vector listings
-were specified for index\ \&\fC3\fP, which eventually led to an entry \fC0:50\fP\&.
-The final symmetrization step will take the \fC[0,3]\fP
-entry of weight\ \&\fC20\fP and combine it with the \fC[3,0]\fP entry
-of weight\ \&\fC50\fP\&. The resulting matrix will then have the \fC[0,3]\fP
-and the \fC[3,0]\fP entry both equal to either the maximum, the sum,
-or the product of the two quantities\ \&\fC50\fP and\ \&\fC20\fP\&.
-.in -2m
-
-.ZI 2m "\fB--quiet-re\fP (\fIquiet for repeated entries\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--quiet-rv\fP (\fIquiet for repeated vectors\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-q\fP (\fIthe two above combined\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Warning options\&. Turn these on if you expect the raw data to be free
-of repeats\&.
-.in -2m
-.SH AUTHOR
-Stijn van Dongen\&.
-.SH SEE ALSO
-\fBmcxio(5)\fP, \fBmcl(1)\fP, \fBmcxload(1)\fP
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxassemble.html b/doc/mcxassemble.html
deleted file mode 100644
index 16280d9..0000000
--- a/doc/mcxassemble.html
+++ /dev/null
@@ -1,522 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
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-{ margin-left: 8%;
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-{ position: relative;
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-{ width: 2em;
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-body
-{ text-align: justify;
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-}
-</style>
-<title>The mcxassemble manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxassemble.ps"><b>mcxassemble</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxassemble — transform raw cooccurrence data to mcl matrix format.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxassemble</b>
-<a class="intern" href="#opt-b"><b>-b</b> base (<i>base name</i>)</a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>write to file fname</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>write output in binary format</i>)<b>]</b></a>
-<a class="intern" href="#opt--map"><b>[--map</b> (<i>apply base.map</i>)<b>]</b></a>
-<a class="intern" href="#opt-raw-tf"><b>[-raw-tf</b> (<i>apply transform spec to input</i>)<b>]</b></a>
-<a class="intern" href="#opt-rv"><b>[-rv</b> MODE (<i>repeated vectors</i>)<b>]</b></a>
-<a class="intern" href="#opt-re"><b>[-re</b> MODE (<i>repeated entries</i>)<b>]</b></a>
-<a class="intern" href="#opt-ri"><b>[-ri</b> MODE (<i>adding mirror image</i>)<b>]</b></a>
-<a class="intern" href="#opt-r"><b>[-r</b> MODE (<i>repeated entries/vectors/images</i>)<b>]</b></a>
-<a class="intern" href="#opt-prm-tf"><b>[-prm-tf</b> (<i>apply transform spec to primary matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-sym-tf"><b>[-sym-tf</b> (<i>apply transform spec to symmetrified matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-q"><b>[-q</b> (<i>quiet mode</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The options above embody the default setup when using mcxassemble.
-There are many more options which mostly provide subtly different
-ways of doing input/output, set warning levels, or regulate
-how repeated entries and vectors should be treated.
-The full list of options is shown below.
-Read <a class="intern" href="#description">DESCRIPTION</a> for learning about mcxassemble input/output
-and the functionality it provides.
-</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-As of release 05-314 <a class="local sibling" href="mcl.html">mcl</a> is able to cluster label-type input
-on the fly. In most cases, this will be sufficient. Alternatively,
-<a class="local sibling" href="mcxload.html">mcxload</a> can be used to map label-type input onto mcl
-matrices. Consequently, there are likely fewer scenarios nowadays
-where <b>mcxassemble</b> is the best solution. Consider first whether
-<b>mcl</b> in label mode or <b>mcxload</b> can do the job as well.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxassemble</b>
-<a class="intern" href="#opt-b"><b>[-b</b> base (<i>base name</i>)<b>]</b></a>
-<a class="intern" href="#opt-hdr"><b>[-hdr</b> fname (<i>read header file</i>)<b>]</b></a>
-<a class="intern" href="#opt-raw"><b>[-raw</b> fname (<i>read raw file</i>)<b>]</b></a>
-<a class="intern" href="#opt--map"><b>[--map</b> (<i>apply base.map</i>)<b>]</b></a>
-<a class="intern" href="#opt--cmap"><b>[--cmap</b> (<i>apply base.cmap</i>)<b>]</b></a>
-<a class="intern" href="#opt--rmap"><b>[--rmap</b> (<i>apply base.rmap</i>)<b>]</b></a>
-<a class="intern" href="#opt-map"><b>[-map</b> fname (<i>apply fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-rmap"><b>[-rmap</b> fname (<i>apply fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-cmap"><b>[-cmap</b> fname (<i>apply fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-tag"><b>[-tag</b> tag (<i>apply base.tag</i>)<b>]</b></a>
-<a class="intern" href="#opt-rtag"><b>[-rtag</b> tag (<i>apply base.tag</i>)<b>]</b></a>
-<a class="intern" href="#opt-ctag"><b>[-ctag</b> tag (<i>apply base.tag</i>)<b>]</b></a>
-<a class="intern" href="#opt-skw"><b>[-skw</b> fname (<i>write skew matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-prm"><b>[-prm</b> fname (<i>write primary result matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--skw"><b>[--skw</b> (<i>write base.skw</i>)<b>]</b></a>
-<a class="intern" href="#opt--prm"><b>[--prm</b> (<i>write base.prm</i>)<b>]</b></a>
-<a class="intern" href="#opt-xo"><b>[-xo</b> suf (<i>write base.suf</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>write to file fname</i>)<b>]</b></a>
-<a class="intern" href="#opt-n"><b>[-n</b> (<i>do not write default symmetrized result</i>)<b>]</b></a>
-<a class="intern" href="#opt-i"><b>[-i</b> (<i>read from single data file</i>)<b>]</b></a>
-<a class="intern" href="#opt-digits"><b>[-digits</b> int (<i>digits width</i>)<b>]</b></a>
-<a class="intern" href="#opt-s"><b>[-s</b> (<i>check for symmetry</i>)<b>]</b></a>
-<a class="intern" href="#opt-raw-tf"><b>[-raw-tf</b> (<i>apply transform spec to input</i>)<b>]</b></a>
-<a class="intern" href="#opt-rv"><b>[-rv</b> <mode> (<i>action for repeated vectors</i>)<b>]</b></a>
-<a class="intern" href="#opt-re"><b>[-re</b> <mode> (<i>action for repeated entries</i>)<b>]</b></a>
-<a class="intern" href="#opt-ri"><b>[-ri</b> <mode> (<i>adding mirror image</i>)<b>]</b></a>
-<a class="intern" href="#opt-r"><b>[-r</b> <mode> (<i>same for entries and vectors</i>)<b>]</b></a>
-<a class="intern" href="#opt-prm-tf"><b>[-prm-tf</b> (<i>apply transform spec to primary matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-sym-tf"><b>[-sym-tf</b> (<i>apply transform spec to symmetrified matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--quiet-re"><b>[--quiet-re</b> (<i>quiet for repeated entries</i>)<b>]</b></a>
-<a class="intern" href="#opt--quiet-rv"><b>[--quiet-rv</b> (<i>quiet for repeated vectors</i>)<b>]</b></a>
-<a class="intern" href="#opt-q"><b>[-q</b> (<i>the two above combined</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxassemble</b> enables easy matrix creation from an intermediate raw matrix
-format that can easily be constructed from a one-pass-parse of cooccurrence
-data. The basic setup is as follows.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Parse cooccurrence data from some external format.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform cooccurrence data to raw mcl data as you parse.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-When done, write out required header and domain information
-to a separate file. The domain information can be built during
-the parsing stage.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use mcxassemble to construct a valid matrix from the raw data
-and the header information.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Nodes can optionally be relabeled by writing a separate map file to be read
-by <b>mcxassemble</b>, which takes the form of a very thin matrix file.
-</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-The easiest thing to do is to group all input/output files under the same
-base name, say <b>base</b>. A standard way of proceeding, which will lead to
-a concise <b>mcxassemble</b> command line, is by creating the input files
-<b>base.raw</b> and <b>base.hdr</b>, and optionally the file <b>base.map</b>. The
-default behaviour of mcxassemble is then to create <b>base.sym</b> as the
-resulting matrix file, containing the symmetrized matrix constructed from
-the raw input.
-</p>
-<p style="margin-bottom:0"><b>Example</b><br>
-Suppose <tt>blastresult</tt> is a file containing blast results.
-The following two commands construct an mcl matrix file from the file.
-</p>
-<div class="verbatim"> mcxdeblast --score=e --sort=a blastresult
- mcxassemble -b blastresult -r max --map</div>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mcxdeblast</b> will generate the
-files <tt>blastresult.hdr</tt>, <tt>blastresult.raw</tt>, and <tt>blastresult.map</tt>.
-The <b>--sort=a</b> option will create a map file corresponding
-with alphabetic ordering. These files are processed by <b>mcxassemble</b>
-and it will generate the file <tt>blastresult.sym</tt>. The <b>-r</b>
-option tells <b>mcxassemble</b> that repeated entries should be maxed;
-each time the largest entry seen thus far will be taken.
-</p>
-<p style="margin-bottom:0"><b>Header file</b><br>
-This file contains a header as usually found in generic mcl matrix files,
-i.e. the required <i>header</i> part, and optionally the <i>domain</i> part(s)
-if not all domains are canonical. Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for more information.
-The domain information in the header file will be used to pre-construct a
-skeleton matrix and to validate the entries in the raw data file as they
-fill the skeleton matrix.
-</p>
-<p style="margin-bottom:0"><b>Raw input format</b><br>
-The file from which raw input is read should have the raw format as
-described in <a class="local sibling" href="mcxio.html">mcxio</a>. Simply put; no header specification, no domain
-specification, and no matrix introduction syntax is used. The file just
-contains a listing of vectors. An example fragment is the following:
-</p>
-<div class="verbatim">2 4:0.34 1:2.8838 4:2.328 1:4.238 1:12 $
-1 2:7.8 $
-2 1:0.01 4:20.3 3:2 $</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The listing of vectors need not be sorted, and neither does
-a vector itself need to be sorted - the mcl generic matrix format
-is actually not different in this respect.
-Furthermore, duplicate entries and duplicate vectors are allowed.
-This is in fact again allowed in the generic format, except
-that where applications expect generic format warnings will be issued and
-duplicate entries will be disregarded. <b>mcxassemble</b> allows customizable
-behaviour dictating how to merge repeated entries.
-Refer to the <a class="intern" href="#opt-re"><b>-re</b>, <b>-rv</b>, <b>-r</b></a>
-options below.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The vectors read by <b>mcxassemble</b> do have to match the domains specified in
-the header file. The leading index that specifies the column index has to be
-present in the column domain; all subsequent indices that specify column
-entries have to be present in the row domain.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<i>If one concatenates the contents of the header file and the data file</i>,
-the result is <i>almost but not quite</i> a file containing a matrix in
-syntactically correct mcl generic matrix format. The parts missing
-are the <tt>(mclmatrix</tt> introduction token, (followed by) the
-<tt>begin</tt> token, and the closing <tt>)</tt> token.
-</p>
-<p style="margin-bottom:0"><b>Map file</b><br>
-This file must contain a map matrix, which is a matrix with the
-following properties:
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The column domain and row domain are of the same cardinality.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Each column has exactly one entry.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Each row domain index occurs in exactly one column.
-</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-Such a matrix is used to relabel the nodes as found in the raw data. A
-situation that might occur when parsing some external format (and producing
-raw matrix format), is that ID's (indices) are handed out on the fly during
-the parse. Afterwards, one may want to relabel the IDs such that they
-correspond with an alphabetic listing of the quantity that is represented by
-the node domain, or by some other sort criterion. A map file is then
-typically generated by the parser, as that is the utility in charge of the
-IDs. A small example of a map file for a graph containing five nodes is the
-following:
-</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 5x5
-)
-(mclmatrix
-begin
-0 4 $ # mno
-1 2 $ # ghi
-2 1 $ # def
-3 3 $ # jkl
-4 0 $ # abc
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This corresponds to a relabeling such that the associated strings
-will be ordered alphabetically. Note that comments can be used
-to link string identifiers with indices. This map file says e.g. that
-the string identifier "mno" is represented by index 0 in the raw data,
-and by index 4 in the matrix output by <b>mcxassemble</b>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade item_leftalign nowrap" ><a name="opt-b"></a><b>-b</b> base (<i>base name</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Base name of files to be processed and output. Refer to <a class="intern" href="#description">DESCRIPTION</a>
-above and the entries of other options below.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-hdr"></a><b>-hdr</b> fname (<i>read header file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-raw"></a><b>-raw</b> fname (<i>read raw file</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Explicitly specify the header file and the data file (rather
-than constructing the file names from a base name and suffixes).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--map"></a><b>--map</b> (<i>apply base.map</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--cmap"></a><b>--cmap</b> (<i>apply base.cmap</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--rmap"></a><b>--rmap</b> (<i>apply base.rmap</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-map"></a><b>-map</b> fname (<i>apply f [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Map options. <b>--cmap</b> combines with the <b>-b</b> option,
-and says that the map file in <b>base</b>.<tt>cmap</tt> (where <b>base</b>
-was specified with <b>-b</b> <b>base</b>) should be applied to the column
-domain only. <b>--rmap</b> works the same for the
-row domain, and <b>--map</b> can be used to apply the same map
-to both the column and row domains.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>-cmap</b> and its siblings are used to explicitly specify the
-map file to be used, rather than combining a base name with a fixed
-suffix.
-<b>-tag</b> and its siblings work in conjuction with
-the <b>-b</b> option, and require that a tag be specified from
-which to construct the map file (by appending it to the base name).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-skw"></a><b>-skw</b> fname (<i>write skew matrix</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-prm"></a><b>-prm</b> fname (<i>write primary result matrix</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--prm"></a><b>--prm</b> (<i>write base.prm</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--skw"></a><b>--skw</ [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Options for writing matrices other than the default symmetrized result.
-The primary result matrix is the matrix constructed from reading in the
-raw data and adding entries to the skeleton matrix as specified
-with the <a class="intern" href="#opt-r"><b>-r</b>, <b>-re</b>, and <b>-rv</b> options</a>.
-This matrix can be written using one of the <b>prm</b> options.
-Calling the primary matrix A, the skew matrix (as defined here)
-is the matrix <tt>A - A^T</tt>, i.e. A minus its transposed matrix.
-It can be written using one of the <b>skw</b> options.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If for some reason the symmetrized result is not needed, its output
-can be prevented using the <b>-n</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-xo"></a><b>-xo</b> suf (<i>write base.suf</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-o"></a><b>-o</b> fname (<i>write to file fname</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-i"></a><b>-i</b> (<i>read from single data file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-digits"></a><b>-digits</b> int (< [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The <b>-xo</b> option is used in conjunction with the <b>-b</b> option
-in order to change the suffix for the file in which the symmetrized
-result matrix is written. Use e.g. <b>-xo</b> <b>mci</b> to change the suffix
-from the default value <tt>sym</tt> to <tt>mci</tt>. Use <b>-o</b> to explicitly
-specify the filename in full. Use <b>-digits</b> to set the number of
-digits written for matrix entries (c.q. edge weights).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-i</b> option is special. It causes
-<b>mcxassemble</b> to read both the header information and the raw data
-from the same file, where the syntax should be fully conforming
-to generic mcl matrix format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-s"></a><b>-s</b> (<i>check for symmetry</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This will check whether the primary result matrix was symmetric.
-It reports the number of failing (or <i>skew</i>) edges.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-raw-tf"></a><b>-raw-tf</b> <tf-spec> (<i>apply transform spec to input</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-prm-tf"></a><b>-prm-tf</b> (<i>apply transform spec to primary matrix</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-sym-tf"></a><b>-sym-tf</b> (<i>apply transform spec to symmetrified matrix</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The first applies its transformation spec to the values
-as found in the raw data. The second applies its transformation
-spec to the primary matrix. The third applies its transformation
-step to the symmetrified matrix.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for documentation on the transformation
-spec syntax.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-rv"></a><b>-rv</b> add|max|min|mul|left|right (<i>action for repeated vectors</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-re"></a><b>-re</b> add|max|min|mul|left|right (<i>action for repeated entries</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ri"></a><b>-ri</b> add|max|min|mul (<i>adding mirror image</i>)</div><div class=" item_ [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Merge options, dictating the behaviour when repeated entries are
-found. A distinction is made between entries that are repeated within
-the same column listing, and entries that are repeated between
-different column listings. An entry can be a repeat of both kinds
-simultaneously as well.
-Additionally, the final result is by default symmetrized by combining with
-the mirror image (in matrix terminology, the <i>transposed</i> matrix). This
-symmetrization can be done in the same variety of ways.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>re</b> option, for repeats within the same column, is carried out
-first. It is applied <i>after</i> the column has its entries sorted, so the
-<tt>left</tt> and <tt>right</tt> options are not garantueed to follow the order found
-in the raw input. The <b>rv</b> option, for repeats over different columns,
-is carried out second.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The option <b>-ri</b> <b>min</b> can assist in implementing
-a (top-list) best reciprocal hit criterion.
-</p>
-<p style="margin-bottom:0"><b>Examples</b><br>
-The column
-</p>
-<div class="verbatim">0 1:30 1:50 2:60 4:70 3:20 1:40 2:40 $</div>
-<p style="margin-top:0em; margin-bottom:0em">
-is encountered in the input, listing entries for the vector labeled
-with index <tt>0</tt>. If <b>-re</b> <b>add</b> or <b>-r</b> <b>add</b>
-is used, it will transform to the vector
-</p>
-<div class="verbatim">0 1:120 2:60 3:20 4:70 $</div>
-<p style="margin-top:0em; margin-bottom:0em">
-If <b>-re</b> <b>max</b> or <b>-r</b> <b>add</b>
-is used instead, it will transform to the vector
-</p>
-<div class="verbatim">0 1:40 2:60 3:20 4:70 $</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Suppose <i>add</i> mode is used, and that later on another
-vector specification for the index <tt>0</tt> is found, leading
-to this transformed vector:
-</p>
-<div class="verbatim">0 1:60 2:80 4:40 $</div>
-<p style="margin-top:0em; margin-bottom:0em">
-If <b>-rv</b> <b>max</b> was specified, this new vector is combined with the
-previous vector by taking the entry wise maximum:
-</p>
-<div class="verbatim">0 1:120 2:60 3:20 4:70 $ # first (transformed) vector
-0 1:60 2:80 4:40 $ # second vector
-
-0 1:120 2:80 3:20 4:70 $ # entry wise maximum</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Finally, suppose that somewhere one or more vector listings
-were specified for index <tt>3</tt>, which eventually led to an entry <tt>0:50</tt>.
-The final symmetrization step will take the <tt>[0,3]</tt>
-entry of weight <tt>20</tt> and combine it with the <tt>[3,0]</tt> entry
-of weight <tt>50</tt>. The resulting matrix will then have the <tt>[0,3]</tt>
-and the <tt>[3,0]</tt> entry both equal to either the maximum, the sum,
-or the product of the two quantities <tt>50</tt> and <tt>20</tt>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--quiet-re"></a><b>--quiet-re</b> (<i>quiet for repeated entries</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--quiet-rv"></a><b>--quiet-rv</b> (<i>quiet for repeated vectors</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-q"></a><b>-q</b> (<i>the two above combined</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Warning options. Turn these on if you expect the raw data to be free
-of repeats.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-Stijn van Dongen.
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcxio.html">mcxio</a>, <a class="local sibling" href="mcl.html">mcl</a>, <a class="local sibling" href="mcxload.html">mcxload</a>
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/mcxclcf.1 b/doc/mcxclcf.1
deleted file mode 100644
index c9bf8c7..0000000
--- a/doc/mcxclcf.1
+++ /dev/null
@@ -1,157 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx clcf" 1 "16 May 2014" "mcx clcf 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx clcf \- compute the clustering coefficient of a graph
-.SH SYNOPSIS
-
-\fBmcx\ \&clcf\fP [options] [matrix-file]
-
-mcxclcf is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIclcf\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcx\ \&clcf\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-imx\fP <fname> (\fIspecify matrix input\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIwrite to this file\fP)\fB]\fP
-\fB[-t\fP <int> (\fIuse <int> threads\fP)\fB]\fP
-\fB[-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)\fB]\fP
-\fB[-j\fP <intj> (\fIthis job has index <intj>\fP)\fB]\fP
-\fB[--summary\fP (\fIreturn mean clustering coefficient\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcx\ \&clcf\fP computes the clustering coefficient of a graph\&.
-
-The input graph/matrix, if specified with the \fB-imx\fP option, has to
-be in mcl matrix/graph format\&. You can use label input instead by using the
-\fB-abc\fP option\&.
-Refer to \fBmcxio(5)\fP for a description of these two input formats\&.
-By default \fBmcx\ \&diameter\fP reads from STDIN \fIand expects matrix format\fP\&.
-To specify label input from STDIN use \fB-abc\fP\ \&\fB-\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input\&. STDIN is assumed if not specified\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file\fP)"
-\&
-.br
-The file name for output\&. STDOUT is the default output stream\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-With \fB-abc\fP this option will, additionally, construct
-a graph only on the labels found in the tab file\&.
-If this option is used in conjunction with \fB-imx\fP the
-tab domain and the matrix domain are required to be identical\&.
-.in -2m
-
-.ZI 2m "\fB--summary\fP (\fIreturn mean clustering coefficient\fP)"
-\&
-.br
-By the default a 1-column table (with row names included) is output, one row
-for each node\&. This option causes the output of the average clustering
-coefficient only\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <int> (\fIuse <int> threads\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-j\fP <intj> (\fIthis job has index <intj>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Computing clustering coefficients is time-intensive
-for large graphs\&. If you have multiple CPUs available consider using as
-many threads\&. Additionally it is possible to spread the computation over
-multiple jobs/machines\&.
-These three options are described in the \fBclmprotocols\fP manual page\&.
-The following set of options, if given to as many commands, defines three jobs, each running four threads\&.
-
-.di ZV
-.in 0
-.nf \fC
--t 4 -J 3 -j 0 -o out\&.0
--t 4 -J 3 -j 1 -o out\&.1
--t 4 -J 3 -j 2 -o out\&.2
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The output can then be collected with
-
-.di ZV
-.in 0
-.nf \fC
-mcx collect --add-column -o out\&.all out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxclcf.html b/doc/mcxclcf.html
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-<title>The mcx clcf manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxclcf.ps"><b>mcx clcf</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx clcf — compute the clustering coefficient of a graph</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx clcf</b> [options] [matrix-file]</p>
-<p style="margin-bottom:0" class="asd_par">mcxclcf is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>clcf</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx clcf</b>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix input</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>write to this file</i>)<b>]</b></a>
-<a class="intern" href="#opt-t"><b>[-t</b> <int> (<i>use <int> threads</i>)<b>]</b></a>
-<a class="intern" href="#opt-J"><b>[-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)<b>]</b></a>
-<a class="intern" href="#opt-j"><b>[-j</b> <intj> (<i>this job has index <intj></i>)<b>]</b></a>
-<a class="intern" href="#opt--summary"><b>[--summary</b> (<i>return mean clustering coefficient</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx clcf</b> computes the clustering coefficient of a graph.</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph/matrix, if specified with the <b>-imx</b> option, has to
-be in mcl matrix/graph format. You can use label input instead by using the
-<b>-abc</b> option.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of these two input formats.
-By default <b>mcx diameter</b> reads from STDIN <i>and expects matrix format</i>.
-To specify label input from STDIN use <b>-abc</b> <b>-</b>.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input. STDIN is assumed if not specified.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for output. STDOUT is the default output stream.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-With <b>-abc</b> this option will, additionally, construct
-a graph only on the labels found in the tab file.
-If this option is used in conjunction with <b>-imx</b> the
-tab domain and the matrix domain are required to be identical.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--summary"></a><b>--summary</b> (<i>return mean clustering coefficient</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-By the default a 1-column table (with row names included) is output, one row
-for each node. This option causes the output of the average clustering
-coefficient only.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-t"></a><b>-t</b> <int> (<i>use <int> threads</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-J"></a><b>-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-j"></a><b>-j</b> <intj> (<i>this job has index <intj></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Computing clustering coefficients is time-intensive
-for large graphs. If you have multiple CPUs available consider using as
-many threads. Additionally it is possible to spread the computation over
-multiple jobs/machines.
-These three options are described in the <a class="local sibling" href="clmprotocols.html">clmprotocols</a> manual page.
-The following set of options, if given to as many commands, defines three jobs, each running four threads.
-</p>
-<div class="verbatim">-t 4 -J 3 -j 0 -o out.0
--t 4 -J 3 -j 1 -o out.1
--t 4 -J 3 -j 2 -o out.2</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output can then be collected with
-</p>
-<div class="verbatim">mcx collect --add-column -o out.all out.[0-2]</div>
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/mcxconvert.1 b/doc/mcxconvert.1
deleted file mode 100644
index 24a2d09..0000000
--- a/doc/mcxconvert.1
+++ /dev/null
@@ -1,114 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx convert" 1 "16 May 2014" "mcx convert 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx convert \- convert between mcx storage types
-.SH SYNOPSIS
-
-\fBmcx\ \&convert\fP <matrix-file-in> <matrix-file-out>
-.br
-\fBmcx\ \&convert\fP [--write-binary] --cone-to-stack <cat-file-in> <cat-file-out>
-.br
-\fBmcx\ \&convert\fP [--write-binary] --stack-to-cone <cat-file-in> <cat-file-out>
-
-mcxconvert is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIconvert\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcx\ \&convert\fP
-\fB[--cone-to-stack\fP (\fItransform cone file to stack file\fP)\fB]\fP
-\fB[--stack-to-cone\fP (\fItransform stack file to cone file\fP)\fB]\fP
-\fB[--write-binary\fP (\fIoutput native binary format\fP)\fB]\fP
-\fB[--cat\fP (\fIread and write cat format\fP)\fB]\fP
-\fB[-cat-max\fP <num> (\fIlimit the stack conversion to <num> matrices\fP)\fB]\fP
-
-In the two-argument invocation without additional arguments, \fBmcx\ \&convert\fP
-converts from the format found in the first file to the other format, i\&.e\&.
-from native interchange to native binary format or the other way around\&. When
-querying with the \fB-q\fP option, mcx{convert} will output a one-line
-synopsis describing the matrix in the argument\&. The
-\fB--cone-to-stack\fP and \fB--stack-to-cone\fP options convert
-between the two types of concatenated output provided by \fBmclcm\fP\&.
-.SH DESCRIPTION
-
-The \fBmcl\fP libraries make extensive use of matrices\&. Matrices
-are used to encode graphs, matrices and clusterings\&.
-They can be stored either in interchange or in binary format\&. The latter is
-somewhat more efficient in storage and much faster in both reading and
-writing, but the default is interchange format\&.
-
-The \fBmcl\fP input routines recognize the type of storage they are dealing
-with\&. If you want to convert a matrix to the other storage type,
-simply specify the file name of the matrix you want to convert\&.
-\fBmcx\ \&convert\fP will recognize its type, and write the other type
-to the file specified as the second argument\&.
-.SH OPTIONS
-
-.ZI 2m "\fB--cone-to-stack\fP (\fItransform cone file to stack file\fP)"
-\&
-.br
-This option requires two trailing options, the names of respectively the
-source cone file and the target stack file\&.
-.in -2m
-
-.ZI 2m "\fB--stack-to-cone\fP (\fItransform stack file to cone file\fP)"
-\&
-.br
-This option requires two trailing options, the names of respectively the
-source stack file and the target cone file\&.
-.in -2m
-
-.ZI 2m "\fB--cat\fP (\fIread and write cat format\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB-cat-max\fP <num> (\fIlimit the stack conversion to <num> matrices\fP)"
-\&
-.br
-.in -2m
-
-.ZI 2m "\fB--write-binary\fP (\fIoutput native binary format\fP)"
-\&
-.br
-This option is only useful with either of the options \fB--cone-to-stack\fP,
-\fB--stack-to-cone\fP, or \fB--cat\fP\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxconvert.html b/doc/mcxconvert.html
deleted file mode 100644
index cb35f35..0000000
--- a/doc/mcxconvert.html
+++ /dev/null
@@ -1,209 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
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-<style type="text/css">
-/* START aephea.base.css */
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-a.intern:link { color: #1111aa; }
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-a.quiet:visited { color: black; }
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-{ font-family: monospace;
-margin-top: 1em;
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-font-size: 10pt;
-margin-left: 2em;
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-<title>The mcx convert manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxconvert.ps"><b>mcx convert</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx convert — convert between mcx storage types</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx convert</b> <matrix-file-in> <matrix-file-out><br>
-<b>mcx convert</b> [--write-binary] --cone-to-stack <cat-file-in> <cat-file-out><br>
-<b>mcx convert</b> [--write-binary] --stack-to-cone <cat-file-in> <cat-file-out>
-</p>
-<p style="margin-bottom:0" class="asd_par">mcxconvert is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>convert</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx convert</b>
-<a class="intern" href="#opt--cone-to-stack"><b>[--cone-to-stack</b> (<i>transform cone file to stack file</i>)<b>]</b></a>
-<a class="intern" href="#opt--stack-to-cone"><b>[--stack-to-cone</b> (<i>transform stack file to cone file</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>output native binary format</i>)<b>]</b></a>
-<a class="intern" href="#opt--cat"><b>[--cat</b> (<i>read and write cat format</i>)<b>]</b></a>
-<a class="intern" href="#opt-cat-max"><b>[-cat-max</b> <num> (<i>limit the stack conversion to <num> matrices</i>)<b>]</b></a>
-</p>
-<p style="margin-bottom:0" class="asd_par">
-In the two-argument invocation without additional arguments, <b>mcx convert</b>
-converts from the format found in the first file to the other format, i.e.
-from native interchange to native binary format or the other way around. When
-querying with the <b>-q</b> option, mcx{convert} will output a one-line
-synopsis describing the matrix in the argument. The
-<b>--cone-to-stack</b> and <b>--stack-to-cone</b> options convert
-between the two types of concatenated output provided by <b>mclcm</b>.
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The <b>mcl</b> libraries make extensive use of matrices. Matrices
-are used to encode graphs, matrices and clusterings.
-They can be stored either in interchange or in binary format. The latter is
-somewhat more efficient in storage and much faster in both reading and
-writing, but the default is interchange format.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>mcl</b> input routines recognize the type of storage they are dealing
-with. If you want to convert a matrix to the other storage type,
-simply specify the file name of the matrix you want to convert.
-<b>mcx convert</b> will recognize its type, and write the other type
-to the file specified as the second argument.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--cone-to-stack"></a><b>--cone-to-stack</b> (<i>transform cone file to stack file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option requires two trailing options, the names of respectively the
-source cone file and the target stack file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--stack-to-cone"></a><b>--stack-to-cone</b> (<i>transform stack file to cone file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option requires two trailing options, the names of respectively the
-source stack file and the target cone file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--cat"></a><b>--cat</b> (<i>read and write cat format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cat-max"></a><b>-cat-max</b> <num> (<i>limit the stack conversion to <num> matrices</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--write-binary"></a><b>--write-binary</b> (<i>output native binary format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option is only useful with either of the options <a class="intern" href="#opt--cone-to-stack"><b>--cone-to-stack</b></a>,
-<a class="intern" href="#opt--stack-to-cone"><b>--stack-to-cone</b></a>, or <a class="intern" href="#opt--cat"><b>--cat</b></a>.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/mcxctty.1 b/doc/mcxctty.1
deleted file mode 100644
index 6dc2008..0000000
--- a/doc/mcxctty.1
+++ /dev/null
@@ -1,195 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx ctty" 1 "16 May 2014" "mcx ctty 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx ctty \- compute betweenness centrality for network nodes or network edges
-.SH SYNOPSIS
-
-\fBmcx\ \&ctty\fP [options] [matrix-file]
-
-mcxctty is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIctty\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcx\ \&ctty\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-imx\fP <fname> (\fIspecify matrix input\fP)\fB]\fP
-\fB[-extent\fP <int> (\fIonly consider paths of length at most <int>\fP)\fB]\fP
-\fB[--edge\fP (\fIcompute edge betweenness centrality\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file name\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[-t\fP <int> (\fIuse <int> threads\fP)\fB]\fP
-\fB[-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)\fB]\fP
-\fB[-j\fP <intj> (\fIthis job has index <intj>\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcx\ \&ctty\fP computes betweenness centrality for all nodes or all edges in a graph, using
-the between centrality update algorithm from [1]\&.
-The program is not yet able to take into account edge weights\&.
-
-The input graph/matrix, if specified with the \fB-imx\fP option, has to
-be in mcl matrix/graph format\&. You can use label input instead by using the
-\fB-abc\fP option\&.
-Refer to \fBmcxio(5)\fP for a description of these two input formats\&.
-By default \fBmcx\ \&diameter\fP reads from STDIN \fIand expects matrix format\fP\&.
-To specify label input from STDIN use \fB-abc\fP\ \&\fB-\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input\&. STDIN is assumed if not specified\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-.br
-The name of the file to write output to\&.
-.in -2m
-
-.ZI 2m "\fB-extent\fP <int> (\fIonly consider paths of length at most <int>\fP)"
-\&
-.br
-This option will lead to different results\&. Results
-will still be informative however, being representative for
-the local context in which nodes reside\&. It does probably not make
-sense to use values smaller than four or five\&.
-.in -2m
-
-.ZI 2m "\fB--edge\fP (\fIcompute edge betweenness centrality\fP)"
-\&
-.br
-The output will be a matrix rather than a labeled list of values\&.
-If the program is split into multiple jobs with the \fB-j\fP
-and \fB-J\fP options, the resulting outputs have to be collated
-using \fCmcx\ \&collect\ \&--add-matrix\fP followed by the respective
-output file names for each of the jobs\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-With \fB-abc\fP this option will, additionally, construct
-a graph only on the labels found in the tab file\&.
-If this option is used in conjunction with \fB-imx\fP the
-tab domain and the matrix domain are required to be identical\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <int> (\fIuse <int> threads\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-j\fP <intj> (\fIthis job has index <intj>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Computing centrality scores in a graph is time-intensive
-for large graphs\&. If you have multiple CPUs available consider using as
-many threads\&. Additionally it is possible to spread the computation over
-multiple jobs/machines\&.
-These three options are described in the \fBclmprotocols\fP manual page\&.
-The following set of options, if given to as many commands, defines three jobs, each running four threads\&.
-
-.di ZV
-.in 0
-.nf \fC
--t 4 -J 3 -j 0 -o out\&.0
--t 4 -J 3 -j 1 -o out\&.1
--t 4 -J 3 -j 2 -o out\&.2
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-For node centrality (the default mode) the output can then be collected with
-
-.di ZV
-.in 0
-.nf \fC
-mcx collect --add-column -o out\&.all out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-For edge centrality (invoked with \fB--edge\fP) the output should be collected with
-
-.di ZV
-.in 0
-.nf \fC
-mcx collect --add-matrix -o out\&.all out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-This collection step is only necessary if the \fB-J\fP was used
-with a value greater than one\&. In particular, if threads were used
-but jobs were not, there will be a single output corresponding to
-the end result\&.
-.in -2m
-.SH REFERENCES
-
-[1]
-Ulrik Brandes, \fIA Faster Algorithm for Betweenness Centrality\fP\&.
-Journal of Mathematical Sociology 25(2): 163-177, (2001)\&.
-http://citeseerx\&.ist\&.psu\&.edu/viewdoc/summary?doi=10\&.1\&.1\&.11\&.2024
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxctty.html b/doc/mcxctty.html
deleted file mode 100644
index a50875c..0000000
--- a/doc/mcxctty.html
+++ /dev/null
@@ -1,253 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
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-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
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-{ width: 2em;
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-body
-{ text-align: justify;
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-</style>
-<title>The mcx ctty manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxctty.ps"><b>mcx ctty</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#references">REFERENCES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx ctty — compute betweenness centrality for network nodes or network edges</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx ctty</b> [options] [matrix-file]</p>
-<p style="margin-bottom:0" class="asd_par">mcxctty is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>ctty</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx ctty</b>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix input</i>)<b>]</b></a>
-<a class="intern" href="#opt-extent"><b>[-extent</b> <int> (<i>only consider paths of length at most <int></i>)<b>]</b></a>
-<a class="intern" href="#opt--edge"><b>[--edge</b> (<i>compute edge betweenness centrality</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-t"><b>[-t</b> <int> (<i>use <int> threads</i>)<b>]</b></a>
-<a class="intern" href="#opt-J"><b>[-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)<b>]</b></a>
-<a class="intern" href="#opt-j"><b>[-j</b> <intj> (<i>this job has index <intj></i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx ctty</b> computes betweenness centrality for all nodes or all edges in a graph, using
-the between centrality update algorithm from <a class="intern" href="#fabc">[1]</a>.
-The program is not yet able to take into account edge weights.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph/matrix, if specified with the <b>-imx</b> option, has to
-be in mcl matrix/graph format. You can use label input instead by using the
-<b>-abc</b> option.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of these two input formats.
-By default <b>mcx diameter</b> reads from STDIN <i>and expects matrix format</i>.
-To specify label input from STDIN use <b>-abc</b> <b>-</b>.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input. STDIN is assumed if not specified.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name of the file to write output to.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-extent"></a><b>-extent</b> <int> (<i>only consider paths of length at most <int></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option will lead to different results. Results
-will still be informative however, being representative for
-the local context in which nodes reside. It does probably not make
-sense to use values smaller than four or five.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--edge"></a><b>--edge</b> (<i>compute edge betweenness centrality</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The output will be a matrix rather than a labeled list of values.
-If the program is split into multiple jobs with the <b>-j</b>
-and <b>-J</b> options, the resulting outputs have to be collated
-using <tt>mcx collect --add-matrix</tt> followed by the respective
-output file names for each of the jobs.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-With <b>-abc</b> this option will, additionally, construct
-a graph only on the labels found in the tab file.
-If this option is used in conjunction with <b>-imx</b> the
-tab domain and the matrix domain are required to be identical.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-t"></a><b>-t</b> <int> (<i>use <int> threads</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-J"></a><b>-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-j"></a><b>-j</b> <intj> (<i>this job has index <intj></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Computing centrality scores in a graph is time-intensive
-for large graphs. If you have multiple CPUs available consider using as
-many threads. Additionally it is possible to spread the computation over
-multiple jobs/machines.
-These three options are described in the <a class="local sibling" href="clmprotocols.html">clmprotocols</a> manual page.
-The following set of options, if given to as many commands, defines three jobs, each running four threads.
-</p>
-<div class="verbatim">-t 4 -J 3 -j 0 -o out.0
--t 4 -J 3 -j 1 -o out.1
--t 4 -J 3 -j 2 -o out.2</div>
-<p style="margin-top:0em; margin-bottom:0em">
-For node centrality (the default mode) the output can then be collected with
-</p>
-<div class="verbatim">mcx collect --add-column -o out.all out.[0-2]</div>
-<p style="margin-top:0em; margin-bottom:0em">
-For edge centrality (invoked with <b>--edge</b>) the output should be collected with
-</p>
-<div class="verbatim">mcx collect --add-matrix -o out.all out.[0-2]</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This collection step is only necessary if the <b>-J</b> was used
-with a value greater than one. In particular, if threads were used
-but jobs were not, there will be a single output corresponding to
-the end result.
-</p>
-</div>
-</div>
-
-<a name="references"></a>
-<h2>REFERENCES</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a name="fabc">[1]</a>
-Ulrik Brandes, <i>A Faster Algorithm for Betweenness Centrality</i>.
-Journal of Mathematical Sociology 25(2): 163-177, (2001).
-<a class="extern" href="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.2024">http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.2024</a>
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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-<title>The mcxdeblast manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxdeblast.ps"><b>mcxdeblast</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#stream">STREAM MODE</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#assemble">ASSEMBLE MODE</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#sealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxdeblast — parse BLAST files and stream
-output directly into mcl or write mcxassemble input.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<b>mcxdeblast</b> file-name
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdeblast</b>
-<a class="intern" href="#opt--score"><b>[--score=</b><b|e|r> (<i>bit scores|e-values|normalize bit score</i>)<b>]</b></a>
-<a class="intern" href="#opt--m9"><b>[--m9</b> (<i>expect BLAST column format</i>)<b>]</b></a>
-<a class="intern" href="#opt--out"><b>[--out</b> <fname> (<i>output file</i>)<b>]</b></a>
-<a class="intern" href="#opt--line-mode"><b>[--line-mode</b> abc (<i>write ID1 ID2 score format</i>)<b>]</b></a>
-<a class="intern" href="#opt--sort"><b>[--sort=</b><a|o> (<i>alphabetic|occurrence sorting</i>)<b>]</b></a>
-<a class="intern" href="#opt--xi-dat"><b>[--xi-dat=</b><suf> (<i>strip <suf> from file-name</i>)<b>]</b></a>
-<a class="intern" href="#opt--xo-dat"><b>[--xo-dat=</b><suf> (<i>add <suf> to base name</i>)<b>]</b></a>
-<a class="intern" href="#opt--bcut"><b>[--bcut=</b><val> (<i>bit score cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--ecut"><b>[--ecut=</b><val> (<i>E-value cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--rcut"><b>[--rcut=</b><val> (<i>raw value cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--tab"><b>[--tab=</b><fname> (<i>tab file</i>)<b>]</b></a>
-<file-name></p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdeblast</b> parses BLAST files.</p>
-<p style="margin-bottom:0" class="asd_par">
-In <i>stream mode</i> mcxdeblast output can be directly streamed to mcl by
-using the mcxdeblast <b>--line-mode</b>=<i>abc</i> option and equipping mcl with
-either <b>--abc</b> or <b>--expect-abc</b>. This can be considered the
-easy, lightweight and fast track. This functionality was recently acquired
-by mcl.</p>
-<p style="margin-bottom:0" class="asd_par">
-In the classic and slightly more heavy-handed <i>assemble mode</i>, mcxdeblast
-creates output files suitable for use by mcxassemble. The latter can in
-turn create input suitable for mcl. This is the mode in which mcxdeblast is
-employed by <b>mclblastline</b>.</p>
-
-<a name="stream"></a>
-<h2>STREAM MODE</h2>
-<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifiying <b>--line-mode</b>=<i>abc</i>.
-Use <b>--m9</b> if the input is in columnar output. Pipe the result
-to a file or directly to mcl. Example invocations can be found
-in <a class="local sibling" href="mcl.html">the mcl manual</a>.</p>
-
-<a name="assemble"></a>
-<h2>ASSEMBLE MODE</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-If the input file is named <tt>iput</tt>, mcxdeblast will by
-default create files <tt>iput.hdr</tt>, <tt>iput.raw</tt>, <tt>iput.tab</tt>,
-<tt>iput.map</tt>, and <tt>iput.err</tt>. The <tt>hdr</tt> file contains
-information about the number of nodes found. It will be read
-by <a class="local sibling" href="mcxassemble.html">mcxassemble</a>. The <tt>raw</tt> file contains the co-occurrence
-scores between different nodes (peptides), also to be
-read by mcxassemble. The co-occurrence scores are in
-terms of mcl indentiers, which are subjected to rearranging
-by mcxassemble in order to correctly align them with the tab file.
-The <tt>tab</tt> file contains bindings between mcl identifiers
-(after rearranging as specified in the map file) and the BLAST labels
-(peptide identifiers). Refer to the manual of <a class="local sibling" href="mcxassemble.html">mcxassemble</a>
-for the syntax of a tab file.
-The <tt>err</tt> file contains a list of any errors encountered.</p>
-<p style="margin-bottom:0" class="asd_par">
-If the <b>--tab</b>=<b>fname</b> option is used mcxdeblast changes
-its behaviour. It will read the file <b>fname</b>, and use
-the bindings found therein. It will no longer output any
-of the <tt>hdr</tt>, <tt>map</tt>, or <tt>tab</tt> files. The <tt>hdr</tt>
-file should be provided by the same application that generated
-the specified tab file, and the <tt>map</tt> file should no longer be
-necessary (it might be convenient though and perhaps the
-future will bring a new <b>--map</b> option).</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--tab</b>=<b>fname</b> option can be convenient e.g. if
-you split a BLAST job over multiple machines and want
-to apply mcxdeblast to each of the subresults. You do
-this by generating a single central tab file in advance.
-Then provide each instance of mcxdeblast with this tab file.
-Each instance will generate a <tt>raw</tt> file. The respective
-<tt>raw</tt> files can simply be concatenated and fed to mcxassemble
-using its <b>-raw</b> option. Additionally, a <tt>hdr</tt> file
-has to be specified for mcxassemble using its <b>-hdr</b>
-option. The syntax of <tt>hdr</tt> files is described in
-the <a class="local sibling" href="mcxassemble.html">mcxassemble</a> manual.
-Currently there is usually only one variable
-in the <tt>hdr</tt> file, which is the number of bindings
-listed in the tab file. This number, in turn, should equal
-the total number of different peptides encountered in the BLAST input.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--tab"></a><b>--tab</b>=<fname> (<i>tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify a tab file to use, rather than automatically generating one.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--out"></a><b>--out</b> <fname> (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the name for the output file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--score"></a><b>--score</b>=<b|e|r> (<i>bit scores|e-values|norm bit score</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify whether to use bit scores, E-values, or bit scores
-normalized by length of the HSP.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--sort"></a><b>--sort</b>=<a|o> (<i>alphabetic|occurrence sorting</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify how to sort labels.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--m9"></a><b>--m9</b> (<i>expect BLAST column format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this option to parse BLAST output formatted with the -m 9 option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--line-mode"></a><b>--line-mode</b>=abc (<i>write ID1 ID2 SCORE format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this to stream output directly into mcl. Here <tt>abc</tt>
-is a literal; <b>--line-mode</b> may acquire other line output
-modes.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xi-dat"></a><b>--xi-dat</b>=<suf> (<i>strip <suf> from <file-name></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If set, the suffix <suf> is stripped from file-name in order
-to obtain the base name for output. If <file-name> does not
-end with suffix, it is assumed to be the base name, and <suf> is
-added in order to obtain the (real) file-name.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-dat"></a><b>--xo-dat</b>=<suf> (<i>add <suf> to base name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Attaches the suffix to the base name. Use this to distinguish
-between different parses. One might for example
-use <b>--score</b>=<i>b</i> <b>--bcut</b>=<i>5</i> <b>--xo-dat</b>=<i>b</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--bcut"></a><b>--bcut</b>=<val> (<i>bit score cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Bit scores below the cutoff value are ignored. This
-triggers the output of bit scores and ignores all other values.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ecut"></a><b>--ecut</b>=<val> (<i>E-value cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-E-values below the cutoff value are ignored. This triggers
-the output of E-values and ignores all other values.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rcut"></a><b>--rcut</b>=<val> (<i>raw value cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Raw values below the cutoff value are ignored. This
-triggers the output of raw values and ignores all other values.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-Stijn van Dongen.
-Jason Stajich implemented the <b>--m9</b> option.
-Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments
-and fixes.
-
-<a name="sealso"></a>
-<h2>SEE ALSO</h2>
-<a class="local sibling" href="mclblastline.html">mclblastline</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>, <a class="local sibling" href="mcl.html">mcl</a>,
-<a class="local sibling" href="clmformat.html">clmformat</a>.
-</body>
-</html>
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diff --git a/doc/mcxdiameter.1 b/doc/mcxdiameter.1
deleted file mode 100644
index c53a461..0000000
--- a/doc/mcxdiameter.1
+++ /dev/null
@@ -1,172 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx diameter" 1 "16 May 2014" "mcx diameter 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
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-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx diameter \- compute the diameter of a graph
-.SH SYNOPSIS
-
-\fBmcx\ \&diameter\fP [options]
-
-mcxdiameter is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIdiameter\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcx\ \&diameter\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-imx\fP <fname> (\fIspecify matrix input\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file name\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[-t\fP <int> (\fIuse <int> threads\fP)\fB]\fP
-\fB[-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)\fB]\fP
-\fB[-j\fP <intj> (\fIthis job has index <intj>\fP)\fB]\fP
-\fB[--summary\fP (\fIoutput diameter and average shortest path length\fP)\fB]\fP
-\fB[--list\fP (\fIlist eccentricity for all nodes\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcx\ \&diameter\fP computes the diameter of a graph\&. The input graph should be
-symmetric\&. Results will be unpredictable for directed graphs\&.
-For label input this is irrelevant as \fBmcx\ \&diameter\fP will create
-a symmetric graph from the input\&.
-
-The input graph/matrix, if specified with the \fB-imx\fP option, has to
-be in mcl matrix/graph format\&. You can use label input instead by using the
-\fB-abc\fP option\&.
-Refer to \fBmcxio(5)\fP for a description of these two input formats\&.
-By default \fBmcx\ \&diameter\fP reads from STDIN \fIand expects matrix format\fP\&.
-To specify label input from STDIN use \fB-abc\fP\ \&\fB-\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input that is in mcl native matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-.br
-The name of the file to write output to\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-With \fB-abc\fP this option will, additionally, construct
-a graph only on the labels found in the tab file\&.
-If this option is used in conjunction with \fB-imx\fP the
-tab domain and the matrix domain are required to be identical\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <int> (\fIuse <int> threads\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-J\fP <intJ> (\fIa total of <intJ> jobs are used\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-j\fP <intj> (\fIthis job has index <intj>\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Computing the diameter of a graph is time-intensive
-for large graphs\&. If you have multiple CPUs available consider using as
-many threads\&. Additionally it is possible to spread the computation over
-multiple jobs/machines\&.
-These three options are described in the \fBclmprotocols\fP manual page\&.
-The following set of options, if given to as many commands, defines three jobs, each running four threads\&.
-
-.di ZV
-.in 0
-.nf \fC
--t 4 -J 3 -j 0 -o out\&.0
--t 4 -J 3 -j 1 -o out\&.1
--t 4 -J 3 -j 2 -o out\&.2
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The output can then be collected with
-
-.di ZV
-.in 0
-.nf \fC
-mcx collect --add-column -o out\&.all out\&.[0-2]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-
-.ZI 2m "\fB--list\fP (\fIlist eccentricity for all nodes\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--summary\fP (\fIoutput diameter and average eccentricity\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The default mode is \fB--list\fP, which results in output
-of the eccentricity of all nodes\&. The eccentricity of
-a node is the distance to any node that is the furthest
-away from it\&. The diameter of a graph is the maximum
-of the eccentricity taken over all nodes in a graph\&.
-In this mode \fBmcx\ \&diameter\fP will not output the diameter
-itself\&. Use \fB--summary\fP to output just the diameter
-and the average eccentricity\&.
-.in -2m
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxdiameter.html b/doc/mcxdiameter.html
deleted file mode 100644
index 961bc8b..0000000
--- a/doc/mcxdiameter.html
+++ /dev/null
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-<title>The mcx diameter manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxdiameter.ps"><b>mcx diameter</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx diameter — compute the diameter of a graph</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx diameter</b> [options]</p>
-<p style="margin-bottom:0" class="asd_par">mcxdiameter is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>diameter</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx diameter</b>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix input</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-t"><b>[-t</b> <int> (<i>use <int> threads</i>)<b>]</b></a>
-<a class="intern" href="#opt-J"><b>[-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)<b>]</b></a>
-<a class="intern" href="#opt-j"><b>[-j</b> <intj> (<i>this job has index <intj></i>)<b>]</b></a>
-<a class="intern" href="#opt--summary"><b>[--summary</b> (<i>output diameter and average shortest path length</i>)<b>]</b></a>
-<a class="intern" href="#opt--list"><b>[--list</b> (<i>list eccentricity for all nodes</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx diameter</b> computes the diameter of a graph. The input graph should be
-symmetric. Results will be unpredictable for directed graphs.
-For label input this is irrelevant as <b>mcx diameter</b> will create
-a symmetric graph from the input.</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph/matrix, if specified with the <b>-imx</b> option, has to
-be in mcl matrix/graph format. You can use label input instead by using the
-<b>-abc</b> option.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of these two input formats.
-By default <b>mcx diameter</b> reads from STDIN <i>and expects matrix format</i>.
-To specify label input from STDIN use <b>-abc</b> <b>-</b>.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in mcl native matrix format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name of the file to write output to.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-With <b>-abc</b> this option will, additionally, construct
-a graph only on the labels found in the tab file.
-If this option is used in conjunction with <b>-imx</b> the
-tab domain and the matrix domain are required to be identical.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-t"></a><b>-t</b> <int> (<i>use <int> threads</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-J"></a><b>-J</b> <intJ> (<i>a total of <intJ> jobs are used</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-j"></a><b>-j</b> <intj> (<i>this job has index <intj></i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Computing the diameter of a graph is time-intensive
-for large graphs. If you have multiple CPUs available consider using as
-many threads. Additionally it is possible to spread the computation over
-multiple jobs/machines.
-These three options are described in the <a class="local sibling" href="clmprotocols.html">clmprotocols</a> manual page.
-The following set of options, if given to as many commands, defines three jobs, each running four threads.
-</p>
-<div class="verbatim">-t 4 -J 3 -j 0 -o out.0
--t 4 -J 3 -j 1 -o out.1
--t 4 -J 3 -j 2 -o out.2</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The output can then be collected with
-</p>
-<div class="verbatim">mcx collect --add-column -o out.all out.[0-2]</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--list"></a><b>--list</b> (<i>list eccentricity for all nodes</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--summary"></a><b>--summary</b> (<i>output diameter and average eccentricity</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The default mode is <b>--list</b>, which results in output
-of the eccentricity of all nodes. The eccentricity of
-a node is the distance to any node that is the furthest
-away from it. The diameter of a graph is the maximum
-of the eccentricity taken over all nodes in a graph.
-In this mode <b>mcx diameter</b> will not output the diameter
-itself. Use <b>--summary</b> to output just the diameter
-and the average eccentricity.
-</p>
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/mcxdump.1 b/doc/mcxdump.1
deleted file mode 100644
index 372861f..0000000
--- a/doc/mcxdump.1
+++ /dev/null
@@ -1,434 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxdump" 1 "16 May 2014" "mcxdump 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxdump \- dump matrices, optionally map indices to labels
-.SH SYNOPSIS
-
-\fBmcxdump\fP
-\fB[-imx\fP <fname> (\fImatrix file\fP)\fB]\fP
-\fB[-icl\fP <fname> (\fIcluster file to be dumped line-wise\fP)\fB]\fP
-\fB[-tf\fP <spec> (\fIapply unary transformations to input matrix\fP)\fB]\fP
-\fB[-imx-cat\fP <fname> (\fIconcatenation matrix file\fP)\fB]\fP
-\fB[-imx-tree\fP <fname> (\fIconcatenation cone file\fP)\fB]\fP
-\fB[--skeleton\fP (\fIread empty matrix, honour domains\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file name (\&'-\&' for stdout)\fP)\fB]\fP
-\fB[-digits\fP <num> (\fIoutput precision\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIrow/column tab (label) file\fP)\fB]\fP
-\fB[-tabc\fP <fname> (\fIcolumn tab file\fP)\fB]\fP
-\fB[-tabr\fP <fname> (\fIrow tab file\fP)\fB]\fP
-\fB[--lazy-tab\fP (\fIallow tab/domain mismatch\fP)\fB]\fP
-\fB[--transpose\fP (\fIwork with the transpose\fP)\fB]\fP
-\fB[--no-values\fP (\fIomit values\fP)\fB]\fP
-\fB[--omit-empty\fP (\fIomit empty columns\fP)\fB]\fP
-\fB[--no-loops\fP (\fIomit loops\fP)\fB]\fP
-\fB[--force-loops\fP (\fIforce loops\fP)\fB]\fP
-\fB[--dump-pairs\fP (\fIemit pairs per line\fP)\fB]\fP
-\fB[--dump-table\fP (\fIdump table format\fP)\fB]\fP
-\fB[-dump-sif\fP <tag> (\fIdump sif format\fP)\fB]\fP
-\fB[-dump-sifx\fP <tag> (\fIdump extended sif format with weights\fP)\fB]\fP
-\fB[--dump-lines\fP (\fIemit rows per line\fP)\fB]\fP
-\fB[--dump-rlines\fP (\fIomit leading identifier\fP)\fB]\fP
-\fB[--dump-vlines\fP (\fIadd leading identifier values\fP)\fB]\fP
-\fB[--dump-lead-off\fP (\fIomit leading identifier\fP)\fB]\fP
-\fB[--dump-lower\fP (\fIdump lower part excluding diagonal\fP)\fB]\fP
-\fB[--dump-loweri\fP (\fIdump lower part including diagonal\fP)\fB]\fP
-\fB[--dump-upper\fP (\fIdump upper part excluding diagonal\fP)\fB]\fP
-\fB[--dump-upperi\fP (\fIdump upper part including diagonal\fP)\fB]\fP
-\fB[--write-tabc\fP (\fIdump tab file on column domain\fP)\fB]\fP
-\fB[--write-tabr\fP (\fIdump tab file on row domain\fP)\fB]\fP
-\fB[--dump-domc\fP (\fIdump column domain\fP)\fB]\fP
-\fB[--dump-domr\fP (\fIdump row domain\fP)\fB]\fP
-\fB[-table-nfields\fP <num> (\fIoutput first <num> fields\fP)\fB]\fP
-\fB[-table-nlines\fP <num> (\fIoutput first <num> lines\fP)\fB]\fP
-\fB[--newick\fP (\fIoutput newick format\fP)\fB]\fP
-\fB[-newick\fP [NBI]+ (\fIexclude Number|Branch-length|Indent\fP)\fB]\fP
-\fB[--write-matrix\fP (\fI(deconcatenate) write matrices\fP)\fB]\fP
-\fB[-split-stem\fP <str> (\fI(deconcatenate) matrices file name stem\fP)\fB]\fP
-\fB[-cat-max\fP <num> (\fI(deconcatenate) write first <num> matrices\fP)\fB]\fP
-\fB[-sep-value\fP <str> (\fInode/value separator\fP)\fB]\fP
-\fB[-sep-field\fP <str> (\fIfield separator\fP)\fB]\fP
-\fB[-sep-lead\fP <str> (\fIlead separator\fP)\fB]\fP
-\fB[-sep-cat\fP <str> (\fIconcatenation separator\fP)\fB]\fP
-\fB[-prefixc\fP <str> (\fIprefix column indices with <str>\fP)\fB]\fP
-\fB[-sort\fP size-{ascending,descending} (\fIvector sort mode\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcxdump\fP reads a data file satisfying the mcl input format
-(refer to \fBmcxio(5)\fP)\&. It outputs a line-based format\&. The
-\fB--dump-pairs\fP option yields a single matrix entry per line,
-identified by the respective column and row identifiers (either index or
-label) separated by the field separator\&.
-The \fB--dump-lines\fP and \fB--dump-rlines\fP result in the
-joining of all row entries on a single line, separated by the field
-separator\&. For both formats, the matrix value corresponding with
-a particular entry is by default output as well\&.
-
-\fBmcxdump\fP can also act on files that contain concatenated
-matrices\&. Refer to the group of options headed by
-\fB-imx-cat\fP\ \&\fIfname\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP <fname> (\fImatrix file\fP)"
-\&
-.br
-Input matrix\&.
-.in -2m
-
-.ZI 2m "\fB-icl\fP <fname> (\fIcluster file\fP)"
-\&
-.br
-This specifies the input matrix, and sets up a cluster-wise line-based label dump\&.
-This option is fully equivalent to the combination of
-\fB--dump-rlines\fP and \fB--no-values\fP\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <spec> (\fIapply unary transformations to input matrix\fP)"
-\&
-.br
-Applies the specified transformation to the matrix before it is output\&.
-Refer to \fBmcxio(5)\fP for a description of the transformation syntax\&.
-.in -2m
-
-.ZI 2m "\fB--transpose\fP (\fIwork with the transpose\fP)"
-\&
-.br
-Work with the tranpsose of the input matrix\&.
-.in -2m
-
-.ZI 2m "\fB--skeleton\fP (\fIread empty matrix, honour domains\fP)"
-\&
-.br
-No entries are read, only domains\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-.br
-Output stream\&. Use \fC-\fP for STDOUT\&.
-.in -2m
-
-.ZI 2m "\fB-digits\fP <num> (\fIoutput precision\fP)"
-\&
-.br
-Specify the precision to use in native interchange format\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIrow/column tab (label) file\fP)"
-\&
-.br
-Substitute column indices and row indices by labels from the tab file\&.
-Since the same tab file is used for both, this implies that the matrix
-domains are identical\&.
-.in -2m
-
-.ZI 2m "\fB-tabc\fP <fname> (\fIcolumn tab file\fP)"
-\&
-.br
-Substitute column indices by labels from the tab file\&.
-.in -2m
-
-.ZI 2m "\fB-tabr\fP <fname> (\fIrow tab file\fP)"
-\&
-.br
-Substitute row indices by labels from the tab file\&.
-.in -2m
-
-.ZI 2m "\fB--lazy-tab\fP (\fIallow tab/domain mismatch\fP)"
-\&
-.br
-If used, the tab file domain(s) do not necessarily need to match
-the corresponding domain in the input matrix\&. Entries missing in
-the tab files will be replaced by a question mark\&.
-.in -2m
-
-.ZI 2m "\fB--no-values\fP (\fIomit values\fP)"
-\&
-.br
-Do not emit values\&.
-.in -2m
-
-.ZI 2m "\fB--omit-empty\fP (\fIomit empty columns\fP)"
-\&
-.br
-Do not output line data (with \fB--dump-table\fP or
-\fB--dump-lines\fP or related options) for those columns
-that are empty\&.
-.in -2m
-
-.ZI 2m "\fB--no-loops\fP (\fIomit loops\fP)"
-\&
-.br
-Do not output entries for which the row index equals the column index,
-if present\&.
-Applies only to matrices for which column and row domains are equal\&.
-.in -2m
-
-.ZI 2m "\fB--force-loops\fP (\fIforce loops\fP)"
-\&
-.br
-For each column, force output of a row entry that matches the
-column index\&.
-Applies only to matrices for which column and row domains are equal\&.
-.in -2m
-
-.ZI 2m "\fB--dump-pairs\fP (\fIemit pairs per line\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-dump-sif\fP <tag> (\fIdump sif format\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-dump-sifx\fP <tag> (\fIdump extended sif format with weights\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-lines\fP (\fIemit rows per line\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-rlines\fP (\fIomit leading column node\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-vlines\fP (\fIadd leading column values\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-lead-off\fP (\fIdo not dump leading identifiers\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-lower\fP (\fIdump lower part excluding diagonal\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-loweri\fP (\fIdump lower part including diagonal\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-upper\fP (\fIdump upper part excluding diagonal\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-upperi\fP (\fIdump upper part including diagonal\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-\fB--dump-pairs\fP is the default mode of output\&. Each matrix entry
-is output as a single pair of column-identifier and row-identifier per line,
-optionally followed by the value of the corresponding matrix entry\&.
-All fields are separated by the field separator\&.
-
-Use \fB-dump-sif\fP\ \&\fI<tag>\fP to dump SIF format\&.
-The argument \fI<tag>\fP will be used as the edge type (the second
-column in SIF format)\&. The option \fB-dump-sifx\fP\ \&\fI<tag>\fP
-is similar except that an extended format is produced where
-the label is followed by the colon character and the edge weight\&.
-
-With \fB--dump-lines\fP, each matrix column is output on a
-single line, with row identifiers separated by the field separator
-and values attached to the row identifier by the node/value separator\&.
-In this format, the column identifier is output as the leading field\&.
-
-\fB--dump-rlines\fP is as \fB--dump-lines\fP,
-except that the column identifier is not output\&.
-Use \fB--dump-lead-off\fP to preclude the output of the leading
-identifiers (for line-based outputs)\&.
-
-\fB--dump-vlines\fP is as \fB--dump-lines\fP\&. The
-leading identifiers are followed by a value associated with
-the entire column\&. This can be used to dump the output
-given by \fBclm vol\fP\&. The value provided is a measure
-for the stability of the cluster that follows\&.
-
-The options pertaining to \fIlower\fP and \fIupper\fP dumps currently
-only work with \fB--dump-pairs\fP\&. They act to only output
-the specified part of the matrix\&.
-.in -2m
-
-.ZI 2m "\fB--dump-table\fP (\fIdump table format\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-table-nfields\fP (\fIfield limit\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-table-nlines\fP (\fIline/row limit\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Output table format\&. In table format no indices are printed by default
-and all values
-are printed including zeroes\&. The options \fB-table-nfields\fP and \fB-table-nlines\fP
-can be used to limit
-the number of fields and lines to be printed\&. Note that fields correspond
-to MCL matrix rows and that lines correspond to MCL matrix columns, as MCL
-calls its primary indices column indices\&.
-Use \fB--dump-lead-off\fP to preclude the output of the leading
-identifiers (for line-based outputs)\&.
-.in -2m
-
-.ZI 2m "\fB--newick\fP (\fIoutput newick format\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-newick\fP [NBI]+ (\fInewick, exclude Number|Branch-length|Indent\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Output a hierarchical clustering specified by \fB-imx-tree\fP
-in Newick tree format\&.
-.in -2m
-
-.ZI 2m "\fB--write-tabc\fP (\fIdump tab file on column domain\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-tabr\fP (\fIdump tab file on row domain\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-domc\fP (\fIdump column domain\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--dump-domr\fP (\fIdump row domain\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options work in conjunction with the \fB-ixm\fP\ \&\fIfname\fP option\&.
-Only the domains from the input matrix are read as if \fB--skeleton\fP
-was specified\&.
-\fB--write-tabc\fP assumes the input tab file envelopes the matrix column
-domain, and it outputs a new tab file restricted to that domain\&.
-\fB--write-tabr\fP acts analogously for the row domain\&.
-\fB--dump-domc\fP and \fB--dump-domr\fP respectively dump the column
-or row domain as a regular dump, outputting labels in case a tab file is
-specified\&.
-
-These options are implemented as ensembles of other options\&.
-For example, \fB--dump-domr\fP \fB-imx\fP\ \&\fIfname\fP corresponds with
-\fB--dump-lines\fP \fB--transpose\fP \fB--skeleton\fP\&.
-.in -2m
-
-.ZI 2m "\fB-imx-cat\fP <fname> (\fIconcatenation matrix file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-imx-tree\fP <fname> (\fIconcatenation cone file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--write-matrix\fP (\fI(deconcatenate) write matrices\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-split-stem\fP <str> (\fI(deconcatenate) matrices file name stem\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cat-max\fP <num> (\fI(deconcatenate) write first <num> matrices\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-\fB-imx-cat\fP is like \fB-imx\fP except that the input is assumed to
-contain multiple concatenated matrices\&.
-The matrices are dumped separated by the
-\fIcat separator\fP (cf\&. \fB-sep-cat\fP)\&.
-Alternatively, the matrices can be written to different files
-using the \fB-split-stem\fP option\&.
-In this case it is possible to output each matrix in native format
-rather than as a dump by specifying \fB--write-matrix\fP\&.
-This makes mcxdump effectively act as a deconcatenator\&.
-In all cases (respectively dumping and writing matrices
-to either the same stream or multiple files) the number of
-matrices to be dumped can be limited with \fB-cat-max\fP\&.
-
-\fB-imx-tree\fP is like \fB-imx-cat\fP except that the input
-is assumed to be in cone format (the format output by \fBmclcm\fP)\&.
-This format encodes a tree as a concatenation of matrices with
-nested domains\&. \fBmcxdump\fP will project all levels of this tree
-so that all row domains are the same as the bottom row domain\&.
-This implies that a set of nested clusterings (on different node
-sets, as the set of clusters of a given level is the node set
-of the next level) is transformed
-into a set of flattened clusterings, all on the same node set\&.
-If you do not want this to happen, simply use \fB-imx-cat\fP\&.
-.in -2m
-
-.ZI 2m "\fB-sep-value\fP <str> (\fInode/value separator\fP)"
-\&
-.br
-Set the node/value separator for line based row ensemble output\&.
-.in -2m
-
-.ZI 2m "\fB-sep-field\fP <str> (\fIfield separator\fP)"
-\&
-.br
-Set the field separator for different row indices in a given column\&.
-.in -2m
-
-.ZI 2m "\fB-sep-lead\fP <str> (\fIlead separator\fP)"
-\&
-.br
-Set the lead separator\&. In the \fB--dump-lines\fP format it
-separates the leading column index from the following ensembl of
-row indices\&. It can be useful to make this different from the
-field separator\&. One can for example grep for columns that have
-more than one entry in a matrix mapping nodes to clusters\&. This
-will find nodes in overlap\&.
-.in -2m
-
-.ZI 2m "\fB-sep-cat\fP <str> (\fIconcatenation separator\fP)"
-\&
-.br
-Set the separator that is used between matrix dumps when a concatenation of
-matrices is dumped\&.
-.in -2m
-
-.ZI 2m "\fB-prefixc\fP <str> (\fIprefix column indices with <str>\fP)"
-\&
-.br
-This can be useful when external row names cannot be numbers and
-when a label dictionary is not available or not appropriate\&.
-.in -2m
-
-.ZI 2m "\fB-sort\fP size-{ascending,descending} (\fIconcatenation separator\fP)"
-\&
-.br
-Reorder the matrix columns prior to dumping, based on the number of
-nonzero entries in each column\&.
-Do not use this in conjunction with a tab file for the column domain\&.
-.in -2m
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcxload(1)\fP,
-\fBmcl(1)\fP,
-\fBmclfaq(7)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxdump.html b/doc/mcxdump.html
deleted file mode 100644
index 7e6f8a0..0000000
--- a/doc/mcxdump.html
+++ /dev/null
@@ -1,452 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
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-body
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-</style>
-<title>The mcxdump manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxdump.ps"><b>mcxdump</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxdump — dump matrices, optionally map indices to labels</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdump</b>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>matrix file</i>)<b>]</b></a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>cluster file to be dumped line-wise</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> <spec> (<i>apply unary transformations to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx-cat"><b>[-imx-cat</b> <fname> (<i>concatenation matrix file</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx-tree"><b>[-imx-tree</b> <fname> (<i>concatenation cone file</i>)<b>]</b></a>
-<a class="intern" href="#opt--skeleton"><b>[--skeleton</b> (<i>read empty matrix, honour domains</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file name ('-' for stdout)</i>)<b>]</b></a>
-<a class="intern" href="#opt-digits"><b>[-digits</b> <num> (<i>output precision</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>row/column tab (label) file</i>)<b>]</b></a>
-<a class="intern" href="#opt-tabc"><b>[-tabc</b> <fname> (<i>column tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-tabr"><b>[-tabr</b> <fname> (<i>row tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt--lazy-tab"><b>[--lazy-tab</b> (<i>allow tab/domain mismatch</i>)<b>]</b></a>
-<a class="intern" href="#opt--transpose"><b>[--transpose</b> (<i>work with the transpose</i>)<b>]</b></a>
-<a class="intern" href="#opt--no-values"><b>[--no-values</b> (<i>omit values</i>)<b>]</b></a>
-<a class="intern" href="#opt--omit-empty"><b>[--omit-empty</b> (<i>omit empty columns</i>)<b>]</b></a>
-<a class="intern" href="#opt--no-loops"><b>[--no-loops</b> (<i>omit loops</i>)<b>]</b></a>
-<a class="intern" href="#opt--force-loops"><b>[--force-loops</b> (<i>force loops</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-pairs"><b>[--dump-pairs</b> (<i>emit pairs per line</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-table"><b>[--dump-table</b> (<i>dump table format</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump-sif"><b>[-dump-sif</b> <tag> (<i>dump sif format</i>)<b>]</b></a>
-<a class="intern" href="#opt-dump-sifx"><b>[-dump-sifx</b> <tag> (<i>dump extended sif format with weights</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-lines"><b>[--dump-lines</b> (<i>emit rows per line</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-rlines"><b>[--dump-rlines</b> (<i>omit leading identifier</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-vlines"><b>[--dump-vlines</b> (<i>add leading identifier values</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-lead-off"><b>[--dump-lead-off</b> (<i>omit leading identifier</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-lower"><b>[--dump-lower</b> (<i>dump lower part excluding diagonal</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-loweri"><b>[--dump-loweri</b> (<i>dump lower part including diagonal</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-upper"><b>[--dump-upper</b> (<i>dump upper part excluding diagonal</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-upperi"><b>[--dump-upperi</b> (<i>dump upper part including diagonal</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-tabc"><b>[--write-tabc</b> (<i>dump tab file on column domain</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-tabr"><b>[--write-tabr</b> (<i>dump tab file on row domain</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-domc"><b>[--dump-domc</b> (<i>dump column domain</i>)<b>]</b></a>
-<a class="intern" href="#opt--dump-domr"><b>[--dump-domr</b> (<i>dump row domain</i>)<b>]</b></a>
-<a class="intern" href="#opt-table-nfields"><b>[-table-nfields</b> <num> (<i>output first <num> fields</i>)<b>]</b></a>
-<a class="intern" href="#opt-table-nlines"><b>[-table-nlines</b> <num> (<i>output first <num> lines</i>)<b>]</b></a>
-<a class="intern" href="#opt--newick"><b>[--newick</b> (<i>output newick format</i>)<b>]</b></a>
-<a class="intern" href="#opt-newick"><b>[-newick</b> [NBI]+ (<i>exclude Number|Branch-length|Indent</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-matrix"><b>[--write-matrix</b> (<i>(deconcatenate) write matrices</i>)<b>]</b></a>
-<a class="intern" href="#opt-split-stem"><b>[-split-stem</b> <str> (<i>(deconcatenate) matrices file name stem</i>)<b>]</b></a>
-<a class="intern" href="#opt-cat-max"><b>[-cat-max</b> <num> (<i>(deconcatenate) write first <num> matrices</i>)<b>]</b></a>
-<a class="intern" href="#opt-sep-value"><b>[-sep-value</b> <str> (<i>node/value separator</i>)<b>]</b></a>
-<a class="intern" href="#opt-sep-field"><b>[-sep-field</b> <str> (<i>field separator</i>)<b>]</b></a>
-<a class="intern" href="#opt-sep-lead"><b>[-sep-lead</b> <str> (<i>lead separator</i>)<b>]</b></a>
-<a class="intern" href="#opt-sep-cat"><b>[-sep-cat</b> <str> (<i>concatenation separator</i>)<b>]</b></a>
-<a class="intern" href="#opt-prefixc"><b>[-prefixc</b> <str> (<i>prefix column indices with <str></i>)<b>]</b></a>
-<a class="intern" href="#opt-sort"><b>[-sort</b> size-{ascending,descending} (<i>vector sort mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdump</b> reads a data file satisfying the mcl input format
-(refer to <a class="local sibling" href="mcxio.html">mcxio</a>). It outputs a line-based format. The
-<b>--dump-pairs</b> option yields a single matrix entry per line,
-identified by the respective column and row identifiers (either index or
-label) separated by the field separator.
-The <b>--dump-lines</b> and <b>--dump-rlines</b> result in the
-joining of all row entries on a single line, separated by the field
-separator. For both formats, the matrix value corresponding with
-a particular entry is by default output as well.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdump</b> can also act on files that contain concatenated
-matrices. Refer to the group of options headed by
-<a class="intern" href="#opt-imx-cat"><b>-imx-cat</b> <i>fname</i></a>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>matrix file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Input matrix.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>cluster file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This specifies the input matrix, and sets up a cluster-wise line-based label dump.
-This option is fully equivalent to the combination of
-<b>--dump-rlines</b> and <b>--no-values</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <spec> (<i>apply unary transformations to input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Applies the specified transformation to the matrix before it is output.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of the transformation syntax.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--transpose"></a><b>--transpose</b> (<i>work with the transpose</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Work with the tranpsose of the input matrix.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--skeleton"></a><b>--skeleton</b> (<i>read empty matrix, honour domains</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-No entries are read, only domains.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output stream. Use <tt>-</tt> for STDOUT.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-digits"></a><b>-digits</b> <num> (<i>output precision</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the precision to use in native interchange format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>row/column tab (label) file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Substitute column indices and row indices by labels from the tab file.
-Since the same tab file is used for both, this implies that the matrix
-domains are identical.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tabc"></a><b>-tabc</b> <fname> (<i>column tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Substitute column indices by labels from the tab file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tabr"></a><b>-tabr</b> <fname> (<i>row tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Substitute row indices by labels from the tab file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--lazy-tab"></a><b>--lazy-tab</b> (<i>allow tab/domain mismatch</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If used, the tab file domain(s) do not necessarily need to match
-the corresponding domain in the input matrix. Entries missing in
-the tab files will be replaced by a question mark.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--no-values"></a><b>--no-values</b> (<i>omit values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Do not emit values.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--omit-empty"></a><b>--omit-empty</b> (<i>omit empty columns</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Do not output line data (with <b>--dump-table</b> or
-<b>--dump-lines</b> or related options) for those columns
-that are empty.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--no-loops"></a><b>--no-loops</b> (<i>omit loops</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Do not output entries for which the row index equals the column index,
-if present.
-Applies only to matrices for which column and row domains are equal.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--force-loops"></a><b>--force-loops</b> (<i>force loops</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-For each column, force output of a row entry that matches the
-column index.
-Applies only to matrices for which column and row domains are equal.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--dump-pairs"></a><b>--dump-pairs</b> (<i>emit pairs per line</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-dump-sif"></a><b>-dump-sif</b> <tag> (<i>dump sif format</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-dump-sifx"></a><b>-dump-sifx</b> <tag> (<i>dump extended sif format with weights</i>)</div><div class=" item_casc [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>--dump-pairs</b> is the default mode of output. Each matrix entry
-is output as a single pair of column-identifier and row-identifier per line,
-optionally followed by the value of the corresponding matrix entry.
-All fields are separated by the field separator.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Use <b>-dump-sif</b> <i><tag></i> to dump SIF format.
-The argument <i><tag></i> will be used as the edge type (the second
-column in SIF format). The option <b>-dump-sifx</b> <i><tag></i>
-is similar except that an extended format is produced where
-the label is followed by the colon character and the edge weight.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-With <b>--dump-lines</b>, each matrix column is output on a
-single line, with row identifiers separated by the field separator
-and values attached to the row identifier by the node/value separator.
-In this format, the column identifier is output as the leading field.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>--dump-rlines</b> is as <b>--dump-lines</b>,
-except that the column identifier is not output.
-Use <b>--dump-lead-off</b> to preclude the output of the leading
-identifiers (for line-based outputs).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>--dump-vlines</b> is as <b>--dump-lines</b>. The
-leading identifiers are followed by a value associated with
-the entire column. This can be used to dump the output
-given by <b>clm vol</b>. The value provided is a measure
-for the stability of the cluster that follows.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The options pertaining to <i>lower</i> and <i>upper</i> dumps currently
-only work with <b>--dump-pairs</b>. They act to only output
-the specified part of the matrix.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--dump-table"></a><b>--dump-table</b> (<i>dump table format</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-table-nfields"></a><b>-table-nfields</b> (<i>field limit</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-table-nlines"></a><b>-table-nlines</b> (<i>line/row limit</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output table format. In table format no indices are printed by default
-and all values
-are printed including zeroes. The options <b>-table-nfields</b> and <b>-table-nlines</b>
-can be used to limit
-the number of fields and lines to be printed. Note that fields correspond
-to MCL matrix rows and that lines correspond to MCL matrix columns, as MCL
-calls its primary indices column indices.
-Use <b>--dump-lead-off</b> to preclude the output of the leading
-identifiers (for line-based outputs).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--newick"></a><b>--newick</b> (<i>output newick format</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-newick"></a><b>-newick</b> [NBI]+ (<i>newick, exclude Number|Branch-length|Indent</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output a hierarchical clustering specified by <b>-imx-tree</b>
-in Newick tree format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-tabc"></a><b>--write-tabc</b> (<i>dump tab file on column domain</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-tabr"></a><b>--write-tabr</b> (<i>dump tab file on row domain</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--dump-domc"></a><b>--dump-domc</b> (<i>dump column domain</i>)</div><div class=" item_cascade item_lef [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options work in conjunction with the <a class="intern" href="#opt-ixm"><b>-ixm</b> <i>fname</i></a> option.
-Only the domains from the input matrix are read as if <a class="intern" href="#opt--skeleton"><b>--skeleton</b></a>
-was specified.
-<b>--write-tabc</b> assumes the input tab file envelopes the matrix column
-domain, and it outputs a new tab file restricted to that domain.
-<b>--write-tabr</b> acts analogously for the row domain.
-<b>--dump-domc</b> and <b>--dump-domr</b> respectively dump the column
-or row domain as a regular dump, outputting labels in case a tab file is
-specified.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-These options are implemented as ensembles of other options.
-For example, <b>--dump-domr</b> <b>-imx</b> <i>fname</i> corresponds with
-<b>--dump-lines</b> <b>--transpose</b> <b>--skeleton</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-imx-cat"></a><b>-imx-cat</b> <fname> (<i>concatenation matrix file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-imx-tree"></a><b>-imx-tree</b> <fname> (<i>concatenation cone file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-matrix"></a><b>--write-matrix</b> (<i>(deconcatenate) write matrices</i>)</div><div class= [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>-imx-cat</b> is like <b>-imx</b> except that the input is assumed to
-contain multiple concatenated matrices.
-The matrices are dumped separated by the
-<i>cat separator</i> (cf. <b>-sep-cat</b>).
-Alternatively, the matrices can be written to different files
-using the <b>-split-stem</b> option.
-In this case it is possible to output each matrix in native format
-rather than as a dump by specifying <b>--write-matrix</b>.
-This makes mcxdump effectively act as a deconcatenator.
-In all cases (respectively dumping and writing matrices
-to either the same stream or multiple files) the number of
-matrices to be dumped can be limited with <b>-cat-max</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>-imx-tree</b> is like <b>-imx-cat</b> except that the input
-is assumed to be in cone format (the format output by <b>mclcm</b>).
-This format encodes a tree as a concatenation of matrices with
-nested domains. <b>mcxdump</b> will project all levels of this tree
-so that all row domains are the same as the bottom row domain.
-This implies that a set of nested clusterings (on different node
-sets, as the set of clusters of a given level is the node set
-of the next level) is transformed
-into a set of flattened clusterings, all on the same node set.
-If you do not want this to happen, simply use <b>-imx-cat</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sep-value"></a><b>-sep-value</b> <str> (<i>node/value separator</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the node/value separator for line based row ensemble output.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sep-field"></a><b>-sep-field</b> <str> (<i>field separator</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the field separator for different row indices in a given column.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sep-lead"></a><b>-sep-lead</b> <str> (<i>lead separator</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the lead separator. In the <b>--dump-lines</b> format it
-separates the leading column index from the following ensembl of
-row indices. It can be useful to make this different from the
-field separator. One can for example grep for columns that have
-more than one entry in a matrix mapping nodes to clusters. This
-will find nodes in overlap.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sep-cat"></a><b>-sep-cat</b> <str> (<i>concatenation separator</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the separator that is used between matrix dumps when a concatenation of
-matrices is dumped.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-prefixc"></a><b>-prefixc</b> <str> (<i>prefix column indices with <str></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This can be useful when external row names cannot be numbers and
-when a label dictionary is not available or not appropriate.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-sort"></a><b>-sort</b> size-{ascending,descending} (<i>concatenation separator</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Reorder the matrix columns prior to dumping, based on the number of
-nonzero entries in each column.
-Do not use this in conjunction with a tab file for the column domain.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxload.html">mcxload</a>,
-<a class="local sibling" href="mcl.html">mcl</a>,
-<a class="local sibling" href="mclfaq.html">mclfaq</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
diff --git a/doc/mcxdump.ps b/doc/mcxdump.ps
deleted file mode 100644
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diff --git a/doc/mcxerdos.1 b/doc/mcxerdos.1
deleted file mode 100644
index 65f33d1..0000000
--- a/doc/mcxerdos.1
+++ /dev/null
@@ -1,173 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx erdos" 1 "16 May 2014" "mcx erdos 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
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-.nr xa -\\w'\\$3'
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-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx erdos \- compute shortest paths in a graph
-.SH SYNOPSIS
-
-\fBmcx\ \&erdos\fP [options]
-
-mcxerdos is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIerdos\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcx\ \&erdos\fP
-\fB[-query\fP <fname> (\fIquery input stream\fP)\fB]\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-imx\fP <fname> (\fIspecify matrix input\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file name\fP)\fB]\fP
-\fB[--is-directed\fP (\fIinput graph is directed\fP)\fB]\fP
-\fB[--is-undirected\fP (\fIinput graph is directed\fP)\fB]\fP
-\fB[-write-path\fP <fname> (\fIpath matrix file\fP)\fB]\fP
-\fB[-write-step\fP <fname> (\fIstep matrix file\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-\fBmcx\ \&erdos\fP computes shortest paths in graphs\&.
-It can read a graph either in label format with \fB-abc\fP
-or in native format with \fB-imx\fP\&.
-It reads pairs of node indices from an input stream, and for
-each pair outputs a data structure describing the full
-set of shortest paths between the two nodes\&.
-Edge weights are not taken into account, so an
-edge always represents a unit step size between two nodes
-irrespective of its weight\&. A mode to compute shortest paths while taking into
-account edge weights will be implemented later as \fBmcx\ \&dijkstra\fP\&.
-
-Note that the full set of shortest paths between two nodes in
-a graph can be described as a directed acyclic graph (DAG),
-and this is how \fBmcx\ \&erdos\fP operates\&. It is easy to construct
-graphs and node pairs for which the number of shortest paths
-between the two nodes becomes exponential in the size of
-the graph, whereas the lattice description is always
-garantueed to map to a subset of the graph edge set\&.
-
-By default it is assumed that the input graph should be treated as
-undirected\&. To this end a transformation step is applied to ensure that the
-graph in memory is undirected\&. It is possible to compute shortest
-paths in directed graphs by using \fB--is-directed\fP, and
-it is possible to omit the transformation step by using \fB--is-undirected\fP\&.
-If the latter is specified while the input graph is in native format and in
-fact directed, results will be erroneous\&. This could in theory be mitigated
-by checking that the input graph is undirected\&. However, the reason to use
-\fB--is-undirected\fP is simply to increase speed of operation, whereas
-such a check would be equally expensive as the transformation step that is
-omitted with \fB--is-undirected\fP\&.
-
-The input graph/matrix, if specified with the \fB-imx\fP option, has to
-be in mcl matrix/graph format\&. You can use label input instead by using the
-\fB-abc\fP option\&.
-Refer to \fBmcxio(5)\fP for a description of these two input formats\&.
-By default \fBmcx\ \&erdos\fP reads from STDIN \fIand expects matrix format\fP\&.
-To specify label input from STDIN use \fB-abc\fP\ \&\fB-\fP\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-query\fP <fname> (\fIquery input\fP)"
-\&
-.br
-The name for the file from which queries are read\&.
-A query consists of two white-space separated node indices
-or two white-space separated labels\&. Labels can only be used
-if either \fB-abc\fP or \fB-tab\fP is specified\&.
-.in -2m
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input that is in mcl native matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-.br
-The name of the file to write output to\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-With \fB-abc\fP this option will, additionally, construct
-a graph only on the labels found in the tab file\&.
-If this option is used in conjunction with \fB-imx\fP the
-tab domain and the matrix domain are required to be identical\&.
-.in -2m
-
-.ZI 2m "\fB--is-directed\fP (\fIcompute directed shortest paths\fP)"
-\&
-.br
-The input graph is not transformed and assumed to be directed\&.
-Shortest paths are computed taking this into account\&.
-.in -2m
-
-.ZI 2m "\fB--is-undirected\fP (\fIskip symmetrification step\fP)"
-\&
-.br
-The input graph is not transformed and assumed to be undirected\&.
-Shortest paths are computed on the assumption that the input
-is undirected\&. Use this option only if you are sure the input
-is undirected and need to have faster execution\&.
-.in -2m
-
-.ZI 2m "\fB-write-path\fP <fname> (\fIpath matrix file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-write-step\fP <fname> (\fIstep matrix file\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The path matrix enumerates the nodes that take
-part in all shortest paths\&. The first list contains
-those nodes that lie at distance 1 of the source node,
-the second list contains nodes lying at distance 2,
-and so on\&.
-The step matrix contains all the edges that make up
-the lattice of shortest paths between the two query nodes\&.
-.in -2m
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxerdos.html b/doc/mcxerdos.html
deleted file mode 100644
index cd6d3c2..0000000
--- a/doc/mcxerdos.html
+++ /dev/null
@@ -1,260 +0,0 @@
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-body
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-<title>The mcx erdos manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxerdos.ps"><b>mcx erdos</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx erdos — compute shortest paths in a graph</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx erdos</b> [options]</p>
-<p style="margin-bottom:0" class="asd_par">mcxerdos is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>erdos</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx erdos</b>
-<a class="intern" href="#opt-query"><b>[-query</b> <fname> (<i>query input stream</i>)<b>]</b></a>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix input</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt--is-directed"><b>[--is-directed</b> (<i>input graph is directed</i>)<b>]</b></a>
-<a class="intern" href="#opt--is-undirected"><b>[--is-undirected</b> (<i>input graph is directed</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-path"><b>[-write-path</b> <fname> (<i>path matrix file</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-step"><b>[-write-step</b> <fname> (<i>step matrix file</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcx erdos</b> computes shortest paths in graphs.
-It can read a graph either in label format with <b>-abc</b>
-or in native format with <b>-imx</b>.
-It reads pairs of node indices from an input stream, and for
-each pair outputs a data structure describing the full
-set of shortest paths between the two nodes.
-Edge weights are not taken into account, so an
-edge always represents a unit step size between two nodes
-irrespective of its weight. A mode to compute shortest paths while taking into
-account edge weights will be implemented later as <b>mcx dijkstra</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Note that the full set of shortest paths between two nodes in
-a graph can be described as a directed acyclic graph (DAG),
-and this is how <b>mcx erdos</b> operates. It is easy to construct
-graphs and node pairs for which the number of shortest paths
-between the two nodes becomes exponential in the size of
-the graph, whereas the lattice description is always
-garantueed to map to a subset of the graph edge set.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-By default it is assumed that the input graph should be treated as
-undirected. To this end a transformation step is applied to ensure that the
-graph in memory is undirected. It is possible to compute shortest
-paths in directed graphs by using <b>--is-directed</b>, and
-it is possible to omit the transformation step by using <b>--is-undirected</b>.
-If the latter is specified while the input graph is in native format and in
-fact directed, results will be erroneous. This could in theory be mitigated
-by checking that the input graph is undirected. However, the reason to use
-<b>--is-undirected</b> is simply to increase speed of operation, whereas
-such a check would be equally expensive as the transformation step that is
-omitted with <b>--is-undirected</b>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph/matrix, if specified with the <b>-imx</b> option, has to
-be in mcl matrix/graph format. You can use label input instead by using the
-<b>-abc</b> option.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of these two input formats.
-By default <b>mcx erdos</b> reads from STDIN <i>and expects matrix format</i>.
-To specify label input from STDIN use <b>-abc</b> <b>-</b>.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-query"></a><b>-query</b> <fname> (<i>query input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name for the file from which queries are read.
-A query consists of two white-space separated node indices
-or two white-space separated labels. Labels can only be used
-if either <b>-abc</b> or <b>-tab</b> is specified.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in mcl native matrix format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The name of the file to write output to.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-With <b>-abc</b> this option will, additionally, construct
-a graph only on the labels found in the tab file.
-If this option is used in conjunction with <b>-imx</b> the
-tab domain and the matrix domain are required to be identical.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--is-directed"></a><b>--is-directed</b> (<i>compute directed shortest paths</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The input graph is not transformed and assumed to be directed.
-Shortest paths are computed taking this into account.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--is-undirected"></a><b>--is-undirected</b> (<i>skip symmetrification step</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The input graph is not transformed and assumed to be undirected.
-Shortest paths are computed on the assumption that the input
-is undirected. Use this option only if you are sure the input
-is undirected and need to have faster execution.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-path"></a><b>-write-path</b> <fname> (<i>path matrix file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-step"></a><b>-write-step</b> <fname> (<i>step matrix file</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The path matrix enumerates the nodes that take
-part in all shortest paths. The first list contains
-those nodes that lie at distance 1 of the source node,
-the second list contains nodes lying at distance 2,
-and so on.
-The step matrix contains all the edges that make up
-the lattice of shortest paths between the two query nodes.
-</p>
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/mcxi.1 b/doc/mcxi.1
deleted file mode 100644
index b3fa115..0000000
--- a/doc/mcxi.1
+++ /dev/null
@@ -1,349 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxi" 1 "16 May 2014" "mcxi 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcx \- a stack language interpreter for interaction with the \fBmcl\fP libraries\&.
-.SH SYNOPSIS
-
-\fBmcxi\fP (enter interactive mode)
-
-\fBmcxi\fP <mcxi expression>
-.SH DESCRIPTION
-
-\fBmcxi\fP can be used both from the command line and interactively, and supports
-a rich set of operations such as transposition, scaling, column scaling,
-multiplication, Hadamard powers and products, et cetera\&. It has variables,
-control primitives, and stack manipulation primitives\&.
-The general aim is to support basic number and matrix arithmetic, as well as
-graph, set, and clustering operations\&. The language will be kept simple,
-and should serve only as a means of making the \fBmcl\fP framework a pleasant one
-for working with graphs, matrices, clusterings, and sets\&.
-The language is typed, and currently has the types \fIinteger, real,
-matrix, string, and block\fP\&.
-Blocks are used both in control statements such as \fBifelse\fP and
-\fBwhile\fP, and for defining compound statements resembling procedures or
-functions\&.
-Some of \fBmcxi\fP\&'s primitives are overloaded\&. The following is a very simple
-example of implementing and using \fBmcl\fP in this language\&.
-
-.di ZV
-.in 0
-.nf \fC
-
- 2\&.0 \&.i def # define inflation value\&.
- /small lm # load matrix in file \&'small\&'\&.
- dim id add # add identity matrix\&.
- st \&.x def # make stochastic, bind to x\&.
- { xpn \&.i infl vm } \&.mcl def # define one mcl iteration\&.
- 20 \&.x \&.mcl repeat # iterate 20 times
- imac # interpret matrix as clustering\&.
- vm # view matrix (clustering)\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Somewhat misleadingly, \&'#\&' is not recognized as a comment
-symbol by \fBmcxi\fP, so don\&'t use it (yet)\&.
-
-\fBmcxi\fP has quite a lot of primitives, and they are not all explained in here\&.
-However, \fBmcxi\fP has several help facilities\&. \fBmcxi\fP\&'s munge modes (command
-line, interactive, and file) are discussed first, followed by some syntactic
-and semantic rules\&.
-Several groups of related primitives are then discussed\&. These are the help
-primitives \fBhelp\fP, \fBgrep\fP, \fBops\fP, and others,
-the binding primitives \fBdef\fP, \fBfree\fP, and \fBunlink\fP,
-the control primitives \fBifelse\fP, \fBdo\fP, \fBrepeat\fP, and \fBwhile\fP,
-and the stack manipulation primitives \fBpop\fP, \fBexch\fP, \fBdup\fP,
-\fBmdup\fP, \fBcopy\fP, \fBroll\fP, \fBclear\fP\&.
-And for the record, \fBmcxi\fP has \fBlt\fP, \fBlq\fP, \fBeq\fP, \fBgq\fP, and
-\fBgt\fP\&.
-In the grandiloquently named \fBINDEX\fP section, you find a list
-of all current \fBmcxi\fP primitives\&.
-
-First, there is no difference as far as \fBmcxi\fP is concerned whether
-you give it a bunch of operators and operands directly from the command
-line, or whether you do it in interactive mode\&. Interactive mode is
-line-based; each time you type a carriage return, \fBmcxi\fP starts interpreting
-the line you typed\&. Newlines can be escaped by preceding them with a
-backslash;
-\fBmcxi\fP will delay interpretation and keep building up your expression\&.
-Command line mode is the same as entering interactive mode and entering a
-single line\&. For non-batch processing, interactive mode is the safest,
-because \fBmcxi\fP will simply refuse to carry out impossible operations,
-whereas in command line mode it will exit\&.
-
-In interactive mode, \fBmcxi\fP will by default list the stack after each line you
-type\&. This is verbosity level 1\&. There are four verbosity levels, namely 0,
-1, 2, and 3 (in increasingly verbose order)\&. Set the level with the \fBvb\fP
-primitive\&. Verbosity control is still a bit crude, this is one of the areas
-in which \fBmcxi\fP will be improved\&.
-
-There is another \fBmcxi\fP munge mode which is entered when reading files
-with the \fBlf\fP (load file) primitive\&. This mode is not line-based,
-the whole file is interpreted in one go \- there is little
-difference with line-based mode\&. Beware though, it is currently
-not possible (nor necessary) to escape newlines in files\&.
-
-Currently, \fBmcxi\fP parses lines of text into atoms in an extremely
-straightforward way: Whitespace is the only separator, and it is always a
-separator\&. This has as a consequence that the block delimiters \fB{\fP and
-\fB}\fP are not allowed to appear next to a non-white character\&. Another
-consequence is that strings cannot contain white spaces\&. Both these
-conditions may be relaxed in the future though\&.
-
-Strings are always entered
-with a leading slash, and anything with a leading slash is a string, so
-\fC/this\fP is a string\&. Currently, the double quote has no special
-meaning, but it may acquire meaning in the future, especially as in
-\fC/"maybe the mcxi future will be brighter"\fP\&.
-
-Variables names are always entered with a leading dot, and anything with a
-leading dot is a variable name\&. Variables are implicitly typed by the
-object to which they are bound\&. There is no support for arrays (yet)\&.
-If variables are used, as in \fC\&.x \&.y add\fP, only the names of
-the variables are popped, and the binding between the names and their
-values stays intact\&.
-
-There are some operators that do in-place modification of the object that
-they act on, such as \fCinfl\fP (inflation)\&. Currently, these are all
-operators acting on matrices\&. When presented with a variable,
-they do change the object associated with the variable\&.
-In the built-in documentation strings (accessible with \fBhelp\fP
-and \fBgrep\fP), such in-place modification is denoted with
-a prime as in \fC<m> -> <m\&'>\fP\&.
-
-\fBdup\fP can be used to duplicate objects\&. In case of variables,
-this will be a copy of the variable name\&. If one occurrence is
-used to free the associated object by some operator, all other
-instances of the variable become \fIstale\fP\&.
-\fBmcxi\fP will notice this and you will see such elements marked as stale
-handles in the stack listing\&. \fBcopy\fP can be used to copy the
-object associated with a variable\&.
-
-\fBmcxi\fP is/interprets a stack language\&. In order to add 1 and 2 you need to
-write \fC1 2 add\fP\&. When add is evaluated, it removes the previous two
-items from the stack and replaces it with their sum, in this case the
-integer 3\&.
-\fBmcxi\fP\&'s types are denoted as \fC<int>\fP, \fC<real>\fP, \fC<mx>\fP,
-\fC<str>\fP, \fC<block>\fP, and so are objects that can be of that type\&. An
-object that is of underspecified type (such as taken by overloaded
-operators) is denoted \fC<obj>\fP\&.
-Where a variable name must occur, \fC<var>\fP is written\&.
-In \fBmcxi\fP parlance a \&'variable\&' is the same as \&'handle\&'\&.
-Remember that a variable named \fCx\fP is written \fC\&.x\fP, and
-that a string "foo" is entered as \fC/foo\fP in \fBmcxi\fP\&.
-.SH OPERATORS
-
-.ZI 2m "\fBhelp\fP"
-\&
-.br
-\fBhelp\fP with no arguments prints a descriptory line for each primitive\&.
-Can only be used at bottom of stack\&.
-Alias: \fBh\fP\&.
-.in -2m
-
-.ZI 2m "\fC/str\fP \fBhelp\fP"
-\&
-.br
-\fBhelp\fP with argument \fC/str\fP prints a descriptive line for the
-primitive named \fCstr\fP\&. The string must be identical to the primitive\&'s
-name, or help will not show anything\&. Alias: \fBh\fP\&.
-.in -2m
-
-.ZI 2m "\fC/str\fP \fBgrep\fP"
-\&
-.br
-Prints each descriptive line in which the string str occurs (literally)\&.
-So \fC/matrix grep\fP should produce a lot of matrix related
-primitives (although it may miss generic primitives such as \fBadd\fP
-and \fBmul\fP)\&. At bottom of stack, prints all descriptive lines\&.
-Alias: \fBg\fP\&.
-.in -2m
-
-.ZI 2m "\fBops\fP"
-\&
-.br
-Lists all primitives and aliases concisely in a paragraph\&.
-.in -2m
-
-.ZI 2m "\fBlist\fP"
-\&
-.br
-Lists the contents of the operand stack\&.
-.in -2m
-
-.ZI 2m "\fBinfo\fP"
-\&
-.br
-Lists the top element of the operand stack\&.
-.in -2m
-
-.ZI 2m "\fC<int>\fP \fBtell\fP"
-\&
-.br
-Lists the top \fC<int>\fP elements of the operand stack\&.
-The trio of \fBlist\fP, \fBinfo\fP, and \fBtell\fP
-is perhaps overdoing it slightly, but anyway there it is\&.
-.in -2m
-
-.ZI 2m "\fBvars\fP"
-\&
-.br
-Lists all variables currently bound\&.
-.in -2m
-
-.ZI 2m "\fC<obj>\fP \fC<var>\fP \fBdef\fP"
-\&
-.br
-Bind \fC<obj>\fP to \fC<var>\fP\&. Redefinition is allowed\&.
-.in -2m
-
-.ZI 2m "\fC<var>\fP \fBfree\fP"
-\&
-.br
-Break the binding between \fC<var>\fP and the object it currently binds,
-and remove object\&.
-.in -2m
-
-.ZI 2m "\fBunlink\fP"
-\&
-.br
-Break the binding between \fC<var>\fP and the object it currently binds,
-and push object on the stack\&.
-.in -2m
-
-.ZI 2m "\fC<int> <block1> <block2>\fP \fBifelse\fP"
-\&
-.br
-If \fC<int>\fP is nonzero execute \fC<block1>\fP,
-otherwise execute \fC<block2>\fP\&.
-The equate operators \fBlt\fP, \fBlq\fP, \fBeq\fP, \fBgq\fP, and \fBgt\fP
-can be used to leave an \fC<int>\fP on the stack\&.
-.in -2m
-
-.ZI 2m "\fC<block>\fP \fBdo\fP"
-\&
-.br
-Execute \fC<block>\fP (one time)\&.
-.in -2m
-
-.ZI 2m "\fC<int> <block>\fP \fBrepeat\fP"
-\&
-.br
-Execute \fC<block>\fP \fC<int>\fP times\&.
-.in -2m
-
-.ZI 2m "\fC<block1> <block2>\fP \fBwhile\fP"
-\&
-.br
-This primitive repeatedly executes the \fIcondition\fP \fC<block1>\fP,
-\fIwhich must push an integer each time it is executed\fP\&. Each time, the
-pushed integer is popped\&. If it was non-zero, \fC<block2>\fP is executed,
-\fC<block1>\fP is executed, and the cycle continues\&. If it was zero,
-\fBwhile\fP is done\&.
-.in -2m
-
-.ZI 2m "\fBpop\fP"
-\&
-.br
-Pops one element off of the stack\&.
-.in -2m
-
-.ZI 2m "\fBexch\fP"
-\&
-.br
-Exchanges the top two elements of the stack\&.
-.in -2m
-
-.ZI 2m "\fBdup\fP"
-\&
-.br
-Duplicates the top element and pushes the duplicate onto the stack\&. In case
-of a variable, the name is duplicated and not the object it points to\&. In
-case of anonymous matrices and strings (and whatever other (composite)
-objects may emerge), a \fIdeep copy\fP is made that is completely independent
-of the original object\&.
-.in -2m
-
-.ZI 2m "\fC<int>\fP \fBmdup\fP"
-\&
-.br
-Duplicates the top \fC<int>\fP elements\&. See the \fBdup\fP entry
-above for the semantics of duplication\&. I wrote \fBmdup\fP because
-I thought some other operator needed it, which turned out to be false\&.
-In the meantime, I became very much attached to \fBmdup\fP,
-so mail me if you think you have any useful use for it\&.
-.in -2m
-
-.ZI 2m "\fBcopy\fP"
-\&
-.br
-Copies the top element and pushes the copy onto the stack\&.
-In case of a variable, copies the object associated with the variable
-rather than the variable\&'s name (as \fBdup\fP would do)\&.
-.in -2m
-
-.ZI 2m "\fC<int1> <int2>\fP \fBroll\fP"
-\&
-.br
-Shift \fC<int1>\fP objects cyclically \fC<int2>\fP times to the right
-if \fC<int2>\fP is positive, to the left otherwise\&.
-.in -2m
-
-.ZI 2m "\fBclear\fP"
-\&
-.br
-Empty the stack\&. All objects bound to variables are unaffected\&.
-.in -2m
-.SH INDEX
-
-This is a list of all \fBmcxi\fP\&'s primitives, including aliases\&.
-Do \&'mcxi /<op> help\&' to see a short descriptive string, where <op>
-is one of the primitives below (remember, strings need a leading slash)\&.
-
-\fBadd\fP \fBaddto\fP \fBcdim\fP \fBch\fP \fBclear\fP \fBcopy\fP \fBdef\fP \fBdgt\fP
-\fBdim\fP \fBdiv\fP \fBdo\fP \fBdup\fP \fBeq\fP \fBexch\fP \fBfree\fP \fBgq\fP
-\fBgrep\fP \fBgt\fP \fBhdm\fP \fBhdp\fP \fBhelp\fP \fBid\fP \fBifelse\fP \fBimac\fP
-\fBinfl\fP \fBinfo\fP \fBjj\fP \fBlf\fP \fBlist\fP \fBlm\fP \fBlq\fP \fBlt\fP \fBmax\fP
-\fBmdup\fP \fBmin\fP \fBmod\fP \fBmul\fP \fBops\fP \fBpop\fP \fBpow\fP \fBquit\fP
-\fBrdim\fP \fBrepeat\fP \fBroll\fP \fBst\fP \fBtell\fP \fBtp\fP \fBtut\fP \fBunlink\fP
-\fBvars\fP \fBvb\fP \fBvm\fP \fBwhile\fP \fBwm\fP \fBxpn\fP \fBbye=quit\fP \fBd=def\fP
-\fBf=free\fP \fBh=help\fP \fBi=info\fP \fBl=list\fP \fBp=pop\fP \fBg=grep\fP
-\fBu=unlink\fP \fBx=exch\fP\&.
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxi.html b/doc/mcxi.html
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-<title>The mcxi manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxi.ps"><b>mcxi</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#operators">OPERATORS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#index">INDEX</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcx — a stack language interpreter for interaction with the <b>mcl</b> libraries.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxi</b> (enter interactive mode)
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxi</b> <mcxi expression>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxi</b> can be used both from the command line and interactively, and supports
-a rich set of operations such as transposition, scaling, column scaling,
-multiplication, Hadamard powers and products, et cetera. It has variables,
-control primitives, and stack manipulation primitives.
-The general aim is to support basic number and matrix arithmetic, as well as
-graph, set, and clustering operations. The language will be kept simple,
-and should serve only as a means of making the <b>mcl</b> framework a pleasant one
-for working with graphs, matrices, clusterings, and sets.
-The language is typed, and currently has the types <i>integer, real,
-matrix, string, and block</i>.
-Blocks are used both in control statements such as <b>ifelse</b> and
-<b>while</b>, and for defining compound statements resembling procedures or
-functions.
-Some of <b>mcxi</b>'s primitives are overloaded. The following is a very simple
-example of implementing and using <b>mcl</b> in this language.
-</p>
-<div class="verbatim">
- 2.0 .i def # define inflation value.
- /small lm # load matrix in file 'small'.
- dim id add # add identity matrix.
- st .x def # make stochastic, bind to x.
- { xpn .i infl vm } .mcl def # define one mcl iteration.
- 20 .x .mcl repeat # iterate 20 times
- imac # interpret matrix as clustering.
- vm # view matrix (clustering).
-</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Somewhat misleadingly, '#' is not recognized as a comment
-symbol by <b>mcxi</b>, so don't use it (yet).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxi</b> has quite a lot of primitives, and they are not all explained in here.
-However, <b>mcxi</b> has several help facilities. <b>mcxi</b>'s munge modes (command
-line, interactive, and file) are discussed first, followed by some syntactic
-and semantic rules.
-Several groups of related primitives are then discussed. These are the help
-primitives <b>help</b>, <b>grep</b>, <b>ops</b>, and others,
-the binding primitives <b>def</b>, <b>free</b>, and <b>unlink</b>,
-the control primitives <b>ifelse</b>, <b>do</b>, <b>repeat</b>, and <b>while</b>,
-and the stack manipulation primitives <b>pop</b>, <b>exch</b>, <b>dup</b>,
-<b>mdup</b>, <b>copy</b>, <b>roll</b>, <b>clear</b>.
-And for the record, <b>mcxi</b> has <b>lt</b>, <b>lq</b>, <b>eq</b>, <b>gq</b>, and
-<b>gt</b>.
-In the grandiloquently named <a class="intern" href="#index">INDEX</a> section, you find a list
-of all current <b>mcxi</b> primitives.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-First, there is no difference as far as <b>mcxi</b> is concerned whether
-you give it a bunch of operators and operands directly from the command
-line, or whether you do it in interactive mode. Interactive mode is
-line-based; each time you type a carriage return, <b>mcxi</b> starts interpreting
-the line you typed. Newlines can be escaped by preceding them with a
-backslash;
-<b>mcxi</b> will delay interpretation and keep building up your expression.
-Command line mode is the same as entering interactive mode and entering a
-single line. For non-batch processing, interactive mode is the safest,
-because <b>mcxi</b> will simply refuse to carry out impossible operations,
-whereas in command line mode it will exit.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-In interactive mode, <b>mcxi</b> will by default list the stack after each line you
-type. This is verbosity level 1. There are four verbosity levels, namely 0,
-1, 2, and 3 (in increasingly verbose order). Set the level with the <b>vb</b>
-primitive. Verbosity control is still a bit crude, this is one of the areas
-in which <b>mcxi</b> will be improved.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-There is another <b>mcxi</b> munge mode which is entered when reading files
-with the <b>lf</b> (load file) primitive. This mode is not line-based,
-the whole file is interpreted in one go — there is little
-difference with line-based mode. Beware though, it is currently
-not possible (nor necessary) to escape newlines in files.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Currently, <b>mcxi</b> parses lines of text into atoms in an extremely
-straightforward way: Whitespace is the only separator, and it is always a
-separator. This has as a consequence that the block delimiters <b>{</b> and
-<b>}</b> are not allowed to appear next to a non-white character. Another
-consequence is that strings cannot contain white spaces. Both these
-conditions may be relaxed in the future though.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Strings are always entered
-with a leading slash, and anything with a leading slash is a string, so
-<tt>/this</tt> is a string. Currently, the double quote has no special
-meaning, but it may acquire meaning in the future, especially as in
-<tt>/"maybe the mcxi future will be brighter"</tt>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Variables names are always entered with a leading dot, and anything with a
-leading dot is a variable name. Variables are implicitly typed by the
-object to which they are bound. There is no support for arrays (yet).
-If variables are used, as in <tt>.x .y add</tt>, only the names of
-the variables are popped, and the binding between the names and their
-values stays intact.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-There are some operators that do in-place modification of the object that
-they act on, such as <tt>infl</tt> (inflation). Currently, these are all
-operators acting on matrices. When presented with a variable,
-they do change the object associated with the variable.
-In the built-in documentation strings (accessible with <b>help</b>
-and <b>grep</b>), such in-place modification is denoted with
-a prime as in <tt><m> -> <m'></tt>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>dup</b> can be used to duplicate objects. In case of variables,
-this will be a copy of the variable name. If one occurrence is
-used to free the associated object by some operator, all other
-instances of the variable become <i>stale</i>.
-<b>mcxi</b> will notice this and you will see such elements marked as stale
-handles in the stack listing. <b>copy</b> can be used to copy the
-object associated with a variable.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxi</b> is/interprets a stack language. In order to add 1 and 2 you need to
-write <tt>1 2 add</tt>. When add is evaluated, it removes the previous two
-items from the stack and replaces it with their sum, in this case the
-integer 3.
-<b>mcxi</b>'s types are denoted as <tt><int></tt>, <tt><real></tt>, <tt><mx></tt>,
-<tt><str></tt>, <tt><block></tt>, and so are objects that can be of that type. An
-object that is of underspecified type (such as taken by overloaded
-operators) is denoted <tt><obj></tt>.
-Where a variable name must occur, <tt><var></tt> is written.
-In <b>mcxi</b> parlance a 'variable' is the same as 'handle'.
-Remember that a variable named <tt>x</tt> is written <tt>.x</tt>, and
-that a string "foo" is entered as <tt>/foo</tt> in <b>mcxi</b>.
-</p>
-
-<a name="operators"></a>
-<h2>OPERATORS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>help</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>help</b> with no arguments prints a descriptory line for each primitive.
-Can only be used at bottom of stack.
-Alias: <b>h</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>/str</tt> <b>help</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<b>help</b> with argument <tt>/str</tt> prints a descriptive line for the
-primitive named <tt>str</tt>. The string must be identical to the primitive's
-name, or help will not show anything. Alias: <b>h</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>/str</tt> <b>grep</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Prints each descriptive line in which the string str occurs (literally).
-So <tt>/matrix grep</tt> should produce a lot of matrix related
-primitives (although it may miss generic primitives such as <b>add</b>
-and <b>mul</b>). At bottom of stack, prints all descriptive lines.
-Alias: <b>g</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>ops</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Lists all primitives and aliases concisely in a paragraph.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>list</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Lists the contents of the operand stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>info</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Lists the top element of the operand stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><int></tt> <b>tell</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Lists the top <tt><int></tt> elements of the operand stack.
-The trio of <b>list</b>, <b>info</b>, and <b>tell</b>
-is perhaps overdoing it slightly, but anyway there it is.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>vars</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Lists all variables currently bound.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><obj></tt> <tt><var></tt> <b>def</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Bind <tt><obj></tt> to <tt><var></tt>. Redefinition is allowed.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><var></tt> <b>free</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Break the binding between <tt><var></tt> and the object it currently binds,
-and remove object.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>unlink</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Break the binding between <tt><var></tt> and the object it currently binds,
-and push object on the stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><int> <block1> <block2></tt> <b>ifelse</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If <tt><int></tt> is nonzero execute <tt><block1></tt>,
-otherwise execute <tt><block2></tt>.
-The equate operators <b>lt</b>, <b>lq</b>, <b>eq</b>, <b>gq</b>, and <b>gt</b>
-can be used to leave an <tt><int></tt> on the stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><block></tt> <b>do</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Execute <tt><block></tt> (one time).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><int> <block></tt> <b>repeat</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Execute <tt><block></tt> <tt><int></tt> times.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><block1> <block2></tt> <b>while</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This primitive repeatedly executes the <i>condition</i> <tt><block1></tt>,
-<i>which must push an integer each time it is executed</i>. Each time, the
-pushed integer is popped. If it was non-zero, <tt><block2></tt> is executed,
-<tt><block1></tt> is executed, and the cycle continues. If it was zero,
-<b>while</b> is done.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>pop</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Pops one element off of the stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>exch</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Exchanges the top two elements of the stack.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>dup</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Duplicates the top element and pushes the duplicate onto the stack. In case
-of a variable, the name is duplicated and not the object it points to. In
-case of anonymous matrices and strings (and whatever other (composite)
-objects may emerge), a <i>deep copy</i> is made that is completely independent
-of the original object.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><int></tt> <b>mdup</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Duplicates the top <tt><int></tt> elements. See the <b>dup</b> entry
-above for the semantics of duplication. I wrote <b>mdup</b> because
-I thought some other operator needed it, which turned out to be false.
-In the meantime, I became very much attached to <b>mdup</b>,
-so mail me if you think you have any useful use for it.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>copy</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Copies the top element and pushes the copy onto the stack.
-In case of a variable, copies the object associated with the variable
-rather than the variable's name (as <b>dup</b> would do).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt><int1> <int2></tt> <b>roll</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shift <tt><int1></tt> objects cyclically <tt><int2></tt> times to the right
-if <tt><int2></tt> is positive, to the left otherwise.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><b>clear</b></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Empty the stack. All objects bound to variables are unaffected.
-</p>
-</div>
-</div>
-
-<a name="index"></a>
-<h2>INDEX</h2>
-<p style="margin-bottom:0" class="asd_par">
-This is a list of all <b>mcxi</b>'s primitives, including aliases.
-Do 'mcxi /<op> help' to see a short descriptive string, where <op>
-is one of the primitives below (remember, strings need a leading slash).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>add</b> <b>addto</b> <b>cdim</b> <b>ch</b> <b>clear</b> <b>copy</b> <b>def</b> <b>dgt</b>
-<b>dim</b> <b>div</b> <b>do</b> <b>dup</b> <b>eq</b> <b>exch</b> <b>free</b> <b>gq</b>
-<b>grep</b> <b>gt</b> <b>hdm</b> <b>hdp</b> <b>help</b> <b>id</b> <b>ifelse</b> <b>imac</b>
-<b>infl</b> <b>info</b> <b>jj</b> <b>lf</b> <b>list</b> <b>lm</b> <b>lq</b> <b>lt</b> <b>max</b>
-<b>mdup</b> <b>min</b> <b>mod</b> <b>mul</b> <b>ops</b> <b>pop</b> <b>pow</b> <b>quit</b>
-<b>rdim</b> <b>repeat</b> <b>roll</b> <b>st</b> <b>tell</b> <b>tp</b> <b>tut</b> <b>unlink</b>
-<b>vars</b> <b>vb</b> <b>vm</b> <b>while</b> <b>wm</b> <b>xpn</b> <b>bye=quit</b> <b>d=def</b>
-<b>f=free</b> <b>h=help</b> <b>i=info</b> <b>l=list</b> <b>p=pop</b> <b>g=grep</b>
-<b>u=unlink</b> <b>x=exch</b>.
-</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-</p>
-and the utilities in the mcl family.
-</body>
-</html>
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-<title>The mcl matrix format specification</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxio.ps"><b>mcxio</b></a>
-14-137
-</p>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxio — the format specifications for input and output in <b>mcl-edge</b></p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The easiest format to create graphs from is a line-based format where each lines
-represents an edge or arc. This format is known as the <i>Large Graph Layout</i>, as
-<i>ncol</i> format (in <i>igraph</i>), and as <i>pairwise</i> format in BioLayout.
-In <b>mcl-edge</b> it is additionally refered to
-as <i>label</i> format or <i>abc</i> format.
-In this format each line has two or three fields. The first two fields
-define the source and destination node of an arc. Such an arc may be
-interpreted as a bidirectional edge, depending on the program reading the format.
-The third field is optional. If present, it should supply a numerical value
-that will be used as edge weights. By default, edge weights are set to one.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Several programs in <b>mcl-edge</b> are able to directly use label format.
-For more elaborate workflows it may be useful to utilise one of the
-native <b>mcl-edge</b> formats that are optimised for interoperability and/or speed.
-The remainder of this manual page documents the format specifications in
-<b>mcl-edge</b>. For hands-on examples of workflows involving both label and other
-formats it may be useful to have a look at <a class="local sibling" href="clmprotocols.html">clmprotocols</a>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The primary objects in the MCL-edge network analysis suite are graphs and
-clusterings. Graphs can be directed and may have loops. Both graphs and
-clusterings are represented in a general unified format. This format
-specifies two domains (a <i>source domain</i> and a <i>destination domain</i>),
-along with lists of arcs linking pairs of elements from the two domains.
-For graphs the two domains are simply both equal to the graph node domain, whereas for
-clusterings one domain is the graph node domain and the other corresponds to
-the enumeration of clusters. Undirected graphs are a special instance of
-a directed graph, where an edge from the undirected graph is represented
-by two arcs of identical weight, one for each possible direction.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The general unified format alluded to above is in fact
-a simple rectangular sparse matrix representation.
-Sparse means that zero entries in the matrix are not stored.
-A zero entry corresponds to an ordered node pair in the graph
-for which no arc exists from the first to the second node.
-An undirected graph corresponds with a symmetric matrix.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The MCL suite uses a slight generalisation of the matrix concept, in
-that the row and column indices (that is, domains) can be arbitrary
-lists of nonnegative integers. Usually, but not necessarily, a domain
-of size <tt>N</tt> will use the common representation of the list
-of integers starting at <tt>0</tt> and ending at <tt>N-1</tt>.
-The <i>source domain</i> is always associated with the columns of
-a matrix, and the <i>destination domain</i> is always associated
-with the rows of a matrix. The matrix format, introduced below,
-first specifies the two domains. It then represents the nonzero matrix
-entries (corresponding with graph arc weights) in a column-wise
-fashion, as a list of lists. For each node from the source domain,
-it presents the list of all its neighbours in the destination domain
-along with the corresponding weights.
-This document describes
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>native matrix format</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The format that can be read in by any mcl application
-expecting a matrix argument. The native format closely resembles
-the layout of matrices as residing in computer memory. There are
-two distinct encodings, respectively <i>interchange</i> and <i>binary</i>.
-Their relative merits are described further below.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>concatenated native matrix format</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This always pertains to matrices in native format concatenated in a single
-file, refered to as a <i>cat file</i>. It is used for example to encode
-hierarchical clusterings as generated by <b>mclcm</b>. A cat file either
-consists of matrices in interchange format or of matrices in binary format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>raw intermediate format</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This is read by <a class="local sibling" href="mcxassemble.html">mcxassemble</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>tab format</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Used by applications such as <a class="local sibling" href="mcl.html">mcl</a> and <a class="local sibling" href="mcxdump.html">mcxdump</a> to
-convert between meaningful labels describing the input data and the
-numerical identifiers used internally.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>label format</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The format used when streaming labels directly into
-<a class="local sibling" href="mcl.html">mcl</a>, various modes of <a class="local sibling" href="mcx.html">mcx</a>, or <a class="local sibling" href="mcxload.html">mcxload</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><i>transformation syntax</i></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The syntax accepted by <a class="local sibling" href="mcl.html">mcl</a>, <a class="local sibling" href="mcxalter.html">mcxalter</a> and
-many other programs to transform graphs and matrices.</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-The interchange format is a portable format that can be transmitted
-across computers and over networks and will work with any version
-of mcl or its sibling programs. It is documented (here) and very stable.
-Applications can easily create matrices in this format.
-The drawback of interchange format is that for very large graphs
-matrix encodings grow very big and are slow to read.</p>
-<p style="margin-bottom:0" class="asd_par">
-The binary format is <i>not</i> garantueed to be portable across
-machines or different versions of mcl or differently compiled
-versions of mcl. Its distinct advantage is that for very large
-graphs the speed advantage over interchange format is dramatic.</p>
-<p style="margin-bottom:0" class="asd_par">
-Conversion between the two formats is easily achieved with
-<b>mcxconvert</b>. Both <a class="local sibling" href="mcl.html">mcl</a> and <a class="local sibling" href="mcxload.html">mcxload</a>
-can save a matrix in either format after constructing it from
-label format.</p>
-<p style="margin-bottom:0" class="asd_par">
-The concatenated format is generated e.g. by <a class="local sibling" href="mclcm.html">mclcm</a> and can
-be transformed by <a class="local sibling" href="mcxdump.html">mcxdump</a> using the <b>-imx-cat</b>
-option. In cat format matrices are simply concatenated,
-so it is easily generated from the command line if needed.
-For native binary format it is imperative that no additional
-bytes are inserted inbetween the matrix encodings. For native
-interchange format the only requirement is that the last
-matrix is followed by nothing but white space.</p>
-<p style="margin-bottom:0" class="asd_par">
-A remark on the sloppy naming conventions used for <b>mcl</b> and its sibling
-utilities may be in order here. The prefix <b>mcx</b> is used for generic
-matrix functionality, the prefix <b>clm</b> is used for generic cluster
-functionaliy. The <i>utility</i> <b>mcx</b> is a general purpose interpreter for
-manipulating matrices (and grahps, sets, and clusterings). The set of all
-<b>mcl</b> siblings (cf. <a class="local sibling" href="mclfamily.html">mclfamily</a>) is loosely refered to as the mcl
-family, which makes use of the mcl libraries (rather than the mcx
-libraries). The full truth is even more horrible, as the mcl/mcx prefix
-conventions used in the C source code follow still other rules.</p>
-<p style="margin-bottom:0" class="asd_par">
-In this document, 'MCL' means 'the mcl setting' or 'the mcl family'. An MCL
-program is one of the programs in the mcl family. The remainder of this
-document contains the following sections.</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#internal">Internal representation of matrices in MCL</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#mspec">Specifying matrices</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#gspec">Specifying graphs</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#raw">Raw format</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#tab">Tab format / label information</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#label">Label format</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">9.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#trans">Transformation syntax</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">10.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">11.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-</div>
-
-<a name="internal"></a>
-<h2>Internal representation of matrices in MCL</h2>
-<p style="margin-bottom:0" class="asd_par">
-There are several aspects to the way in which MCL represents matrices.
-Internally, indices never act as an ofset in an array, and neither do they
-participate in ofset computations. This means that they purely act as
-identifiers. The upshot is that matrices can be handled in which the index
-domains are <i>non-sequential</i> (more below). Thus one can work with
-different graphs and matrices all using subsets of the same set of
-indices/identifiers. This aids in combining data sets in different ways and
-easily comparing the respective results when experimenting. Secondly, only
-<i>nonzero values</i> (and their corresponding indices) are stored. Thirdly,
-MCL stores a matrix as a listing of columns. Iterating over a column is
-trivial; iterating over a row requires a costly transposition computation.
-The last two points should matter little to the user of MCL programs.</p>
-<p style="margin-bottom:0" class="asd_par">
-In textbook expositions and in many matrix manipulation implementations,
-matrices are represented with sequentially indexed rows and columns, with
-the indices usually starting at either zero or one. In the MCL setting, the
-requirement of sequentiality is dropped, and it follows naturally that no
-requirement is posed on the first index. The only requirement MCL poses on
-the indices is that they be nonnegative, and can be represented by the
-integer type used by MCL. On many machines, the largest allowable integer
-will be 2147483647.</p>
-<p style="margin-bottom:0" class="asd_par">
-MCL associates two domains with a matrix <tt>M</tt>, the row domain and column
-domain. The matrix <tt>M</tt> can only have entries <tt>M[i,j]</tt> where <tt>i</tt> is
-in the row domain and <tt>j</tt> is in the column domain. This is vital when
-specifying a matrix: it is illegal to specify an entry <tt>M[i,j]</tt> violating
-this condition. However, it is not necessary to specify <i>all</i>
-entries <tt>M[i,j]</tt> for all possible combinations of <tt>i</tt> and <tt>j</tt>. One
-needs only specify those entries for which the value is nonzero, and only
-nonzero values will be stored internally. In the MCL matrix format, the
-matrix domains must be specified explicitly if they are not canonical (more
-below).</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>Strictly as an aside</b>, the domains primarily exist to ensure data
-integrity. When combining matrices with addition or multiplication (e.g.
-using the <b>mcx</b> utility), MCL will happily combine matrices for which the
-domains do not match, although it will usually issue a warning.
-Conceptually, matrices auto-expand to the dimensions required for the
-operation. Alternatively, a matrix can be viewed as an infinite quadrant,
-with the domains delimiting the parts in which nonzero entries may exist.
-In the future, facilities could be added to MCL (c.q. <b>mcx</b>) to allow for
-placing strict domain requirements on matrices when submitted to binary
-operations such as addition and multiplication.</p>
-
-<a name="mspec"></a>
-<h2>Specifying matrices</h2>
-<p style="margin-bottom:0" class="asd_par">
-From here on, all statements about matrices and graphs are really statements
-about matrices and graphs <i>in the MCL setting</i>. The <i>specification</i>
-of a matrix quite closely matches the internal representation.</p>
-<p style="margin-bottom:0" class="asd_par">
-A matrix M has two domains: the column domain and the row domain. Both
-simply take the form of a set (represented as an ordered list) of indices. A
-<i>canonical domain</i> is a domain of some size <tt>K</tt> where the indices are
-simply the first <tt>K</tt> nonnegative integers <tt>0,1..,K-1</tt>. The domains
-dictate which nonzero entries are allowed to occur in a matrix; only entries
-M[i,j] are allowed where i is in the row domain and j is in the column
-domain.</p>
-<p style="margin-bottom:0" class="asd_par">
-The matrix M is specified in three parts, for which the second is optional.
-The parts are:</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " >Header specification</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This specifies the dimensions K and L of the matrix, where K is the
-size of the row domain, and L is the size of the column domain.
-It looks as follows:</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 9x14
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This dictates that a matrix will be specified for which the row
-domain has dimension 9 and the column domain has dimension 14.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >Domain specification</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The domain specification can have various forms: if nothing is specified,
-the matrix will have canonical domains and a canonical representation,
-similar to the representation encountered in textbooks. Alternatively, the
-row and column domains can each be specified separately, and it is also
-possible to specify only one of them; the other will simply be a canonical
-domain again. Finally, it is possible to declare the two domains identical
-and specify them simultaneously. It is perfectly legal in each case to
-explicitly specify a canonical domain. It is <i>required</i> in each case
-that the number of indices listed in a domain corresponds with the dimension
-given in the header.</p>
-<p style="margin-bottom:0" class="asd_par">
-An example where both a row domain and a column domain are specified:</p>
-<div class="verbatim">(mclrows
- 100 200 300 400 500 600 700 800 900 $
-)
-(mclcols
- 30 32 34 36 38 40 42 44 46 48 50 52 56 58 $
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This example combines with the header given above, as the dimensions fit.
-Had the row domain specification been omitted, the row domain would
-automatically be set to the integers <tt>0,1,..8</tt>. Had the column
-specification been omitted, it would be set to <tt>0,1,..13</tt>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Suppose now that the header did specify the dimensions 10x10.
-Because the dimensions are identical, this raises the possibility
-that the domains be identical.
-A valid way to specify the row domain and column domain in one go is this.</p>
-<div class="verbatim">(mcldoms
- 11 22 33 44 55 66 77 88 99 100 $
-)</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >Matrix specification</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The matrix specification starts with the sequence</p>
-<div class="verbatim">(mclmatrix
-begin</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The 'begin' keyword in the '(mclmatrix' part is followed by a list of
-listings, where the primary list ranges over all column indices in M (i.e.
-indices in the column domain), and where each secondary lists encodes all
-positive entries in the corresponding column. A secondary list (or matrix
-column) starts with the index c of the column, and then contains a listing
-of all row entries in c (these are matrix entries M[r,c] for varying r). The
-entry M[r,c] is specified either as 'r' or as 'r:f', where f is a float. In
-the first case, the entry M[r,c] defaults to 1.0, in the second case, it is
-set to f. The secondary list is closed with the `$' character. A full
-fledged examples thus looks as follows:</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 12x3
-)
-(mclrows
- 11 22 33 44 55 66 77 88 99 123 456 2147483647 $
-)
-(mclcols
- 0 1 2 $
-)
-(mclmatrix
-begin
-0 44 88 99 456 2147483647 $
-1 11 66 77 123 $
-2 22 33 55 $
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Note that the column domain is canonical; its specifiation could have been
-omitted. In this example, no values were specified. See below for more.</p>
-</div>
-</div>
-
-<a name="gspec"></a>
-<h2>Specifying graphs</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-A graph is simply a matrix where the row domain is the same as the column
-domain. Graphs should have positive entries only. Example:</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 12x12
-)
-(mcldoms
-11 22 33 44 55 66 77 88 99 123 456 2147483647 $
-)
-(mclmatrix
-begin
-11 22:2 66:3.4 77:3 123:8 $
-22 11:2 33:3.8 55:8.1 $
-33 22:3.8 44:7 55:6.2 $
-44 33:7 88:5.7 99:7.0 456:3 $
-55 22:8.1 33:6.2 77:2.9 88:3.0 $
-66 11:3.4 123:5.1 $
-77 11:3 55:2.9 123:1.5 $
-88 44:5.7 55:3.0 99:3.0 456:4.2 $
-99 44:7.0 88:3.0 456:1.8 2147483647:3.9 $
-123 11:8 66:5.1 77:1.5 $
-456 44:3 88:4.2 99:1.8 2147483647:6.3 $
-2147483647 99:3.9 456:6.3 $
-)</div>
-<p style="margin-top:0em; margin-bottom:0em">
-Incidentally, clustering this graph with mcl, using default parameters,
-yields a cluster that is represented by the 12x3 matrix shown earlier.</p>
-<p style="margin-bottom:0" class="asd_par">
-The following example shows the same graph, now represented on a
-canonical domain, and with all values implicitly set to 1.0:</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 12x12
-)
-(mclmatrix
-begin
-0 1 5 6 9 $
-1 0 2 4 $
-2 1 3 4 $
-3 2 7 8 10 $
-4 1 2 6 7 $
-5 0 9 $
-6 0 4 9 $
-7 3 4 8 10 $
-8 3 7 10 11 $
-9 0 5 6 $
-10 3 7 8 11 $
-11 8 10 $
-)</div>
-<p style="margin-bottom:0"><b>Additional notes</b><br>
-There are few restrictions on the format that one might actually expect.
-Vectors and entries may occur in any order and need not be sorted.
-Repeated entries and repeated vectors are allowed but are always
-discarded while an error message is emitted.</p>
-<p style="margin-bottom:0" class="asd_par">
-If you want <i>functionally interesting behaviour</i> in combining
-repeated vectors and repeated entries, have a look at the next section
-and at <a class="local sibling" href="mcxassemble.html">mcxassemble</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Within the vector listing, the '#' is a token that introduces
-a comment until the end of line.</p>
-
-<a name="raw"></a>
-<h2>Raw format</h2>
-<p style="margin-bottom:0" class="asd_par">
-A file in <i>raw format</i> is simply a listing of vectors without any
-sectioning structure. No header specification, no domain specification, and
-no matrix introduction syntax is used - these are supplied to the processing
-application by other means. The end-of-vector token '$' must still be used,
-and the comment token '#' is still valid. <a class="local sibling" href="mcxassemble.html">mcxassemble</a>
-imports a file in raw
-format, creates a native matrix from the data therein, and writes the
-matrix to (a different) file. It allows customizable behaviour in how to
-combine repeated entries and repeated vectors. This is typically used in the
-following procedure. A) Do a one-pass-parse on some external cooccurrence
-file/format, generate raw data during the parse and write it to file
-(without needing to build a huge data structure in memory). B) mcxassemble
-takes the raw data and assembles it according to instruction into a native
-mcl matrix.</p>
-
-<a name="tab"></a>
-<h2>Tab format / label information</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Several mcl programs accept options such as <b>-tab</b>, <b>-tabc</b>,
-<b>-tabr</b>, <b>-use-tab</b>, <b>-strict-tab</b>,
-and <b>-extend-tab</b>.
-The argument to these options is invariably the name of
-a so-called <i>tab file</i>.
-Tab files are used to convert between labels (describing entities
-in the data) and indices as used in the mcl matrix format.
-In a tab file each line starts with a unique number which presumably
-corresponds to an index used in a matrix file.
-The rest of the line contains a
-descriptive string associated with the number. It is required
-that each string is unique, although not all mcl programs enforce
-this at the time of writing.
-The string may contain spaces.
-Lines starting with
-<tt>#</tt> are considered comment and are disregarded.
-</p>
-<p style="margin-bottom:0"><b>Tab domain</b><br>The ordered set of indices found in the tab file
-is called the <i>tab domain</i>.</p>
-<p style="margin-bottom:0" class="asd_par">
-Tab files are almost always employed in conjunction with an mcl matrix file.
-<a class="local sibling" href="mcxdump.html">mcxdump</a> and <a class="local sibling" href="clmformat.html">clmformat</a> require by
-default that the tab domain coincides with the matrix domain (either row or
-column or both) to which they will be applied. This can be relaxed for
-either by supplying the <b>--lazy-tab</b> option.</p>
-<p style="margin-bottom:0" class="asd_par">
-mcl provides explicit modes for dealing with tab structures by means of
-the <b>-extend-tab</b>, <b>-restrict-tab</b> and
-<b>-strict-tab</b> options. Refer to the <a class="local sibling" href="mcl.html">mcl</a>
-documentation.</p>
-
-<a name="label"></a>
-<h2>Label format</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Label format is a line based input where two nodes and an optional value are
-specified on each line. The nodes should be specified by labels. If the
-labels contain spaces they should be separated by tabs (and the value if
-present should be separated from the second label by a tab as well). The
-parse code will assume tab-separated labels if it sees a tab character in
-the input, otherwise it will split the input on any kind of whitespace.
-Any line where the first non-whitespace character is the octothorp (#) is
-ignored. The following is an example of label format.</p>
-<div class="verbatim">---8<------8<------8<------8<------8<---
-# the cat and the hat example
-cat hat 0.2
-hat bat 0.16
-bat cat 1.0
-bat bit 0.125
-bit fit 0.25
-fit hit 0.5
-hit bit 0.16
---->8------>8------>8------>8------>8---</div>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcl.html">mcl</a> can read in label format and cluster it when it is
-given the <b>--abc</b> option. It can optionally save
-the input graph in native format and save the label information
-in a tab file with the <b>-save-graph</b> and <b>-save-tab</b>
-options.</p>
-<p style="margin-bottom:0" class="asd_par">
-Refer to the <a class="local sibling" href="mcl.html#started">MCL getting started</a> and
-<a class="local sibling" href="mcl.html#examples">MCL manual examples</a> sections
-for more information on how MCL deals with label format.</p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxload.html">mcxload</a> is a general purpose program for reading
-in label data and other stream formats. It
-encodes them in native mcl format and tab files.
-It allows intermediate transformations on the values.</p>
-
-<a name="trans"></a>
-<h2>Transformation syntax</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcl.html">mcl</a>, <a class="local sibling" href="mcxload.html">mcxload</a>, <a class="local sibling" href="mcxsubs.html">mcxsubs</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>
-and <a class="local sibling" href="mcxalter.html">mcxalter</a>
-all accept the same transformation language in their
-respective <b>tf</b>-type options and mcxsub's <b>val</b>
-specification.</p>
-<p style="margin-bottom:0" class="asd_par">
-A statement in this language is simply a comma-separated
-list of functions accepting a single numerical value.
-The syntax of a function invocation in general is
-<b>func</b>(<i>arg</i>).
-The functions <b>exp</b>, <b>log</b>, <b>neglog</b> can
-also be given an empty parameter list, indicating that
-<i>e</i> is taken as the exponent base. In this case,
-the invocation looks like <b>func</b>().
-Functions with names that start with <tt>#</tt> operate
-on graphs in their entirety. For example, <tt>#knn(50)</tt>
-indicates the k-Nearest Neighbour transformation for
-<tt>k=50</tt>.
-All other names encode functions that operate
-directly on edges.
-Functions with names that start with <tt>#arc</tt> operate
-on directed graphs and yield directed graphs.
-Most of the other <tt>#</tt> functions either expect
-an undirected graph (such as <tt>#knn()</tt>) or yield
-an undirected graph (such as <tt>#add()</tt> and <tt>#max()</tt>.
-The following are supported.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign nowrap " >lt</div></div>
-<div class=" item_text " style="margin-left:12em">
-Filter out values greater than or equal to arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >lq</div></div>
-<div class=" item_text " style="margin-left:12em">
-Filter out values greater than arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >gq</div></div>
-<div class=" item_text " style="margin-left:12em">
-Filter out values less than arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >gt</div></div>
-<div class=" item_text " style="margin-left:12em">
-Filter out values less than or equal to arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >ceil</div></div>
-<div class=" item_text " style="margin-left:12em">
-Set everything higher than arg to arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >floor</div></div>
-<div class=" item_text " style="margin-left:12em">
-Set everything lower than arg to arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >mul</div></div>
-<div class=" item_text " style="margin-left:12em">
-Multiply values by arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >add</div></div>
-<div class=" item_text " style="margin-left:12em">
-Add arg to values.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >power</div></div>
-<div class=" item_text " style="margin-left:12em">
-Raise values to power arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >exp</div></div>
-<div class=" item_text " style="margin-left:12em">
-Raise arg (<i>e</i> if omitted) to value.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >log</div></div>
-<div class=" item_text " style="margin-left:12em">
-Take log in base arg (<i>e</i> if omitted).
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >neglog</div></div>
-<div class=" item_text " style="margin-left:12em">
-Take minus log in base arg (<i>e</i> if omitted).
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >rand</div></div>
-<div class=" item_text " style="margin-left:12em">
-Keep arc with probablity arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >scale</div></div>
-<div class=" item_text " style="margin-left:12em">
-Divide values by arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >abs</div></div>
-<div class=" item_text " style="margin-left:12em">
-Replace value by its absolute value.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >acos</div></div>
-<div class=" item_text " style="margin-left:12em">
-Take acos of value.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#knn</div></div>
-<div class=" item_text " style="margin-left:12em">
-k-Nearest Neighbour reduction with <tt>k=arg</tt> (intersect lists).
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#knnj</div></div>
-<div class=" item_text " style="margin-left:12em">
-As <tt>#knn</tt> above, but join selected neighbour lists.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#ceilnb</div></div>
-<div class=" item_text " style="margin-left:12em">
-Cap number of neighbours at arg at most.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#ils</div></div>
-<div class=" item_text " style="margin-left:12em">
-Inverted log-weight similarity (no argument).
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#mcl</div></div>
-<div class=" item_text " style="margin-left:12em">
-Cluster with inflation=arg, yields induced graph.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#add</div></div>
-<div class=" item_text " style="margin-left:12em">
-Convert two arcs to one edge using addition.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#min</div></div>
-<div class=" item_text " style="margin-left:12em">
-Convert two arcs to one edge using minimum.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#max</div></div>
-<div class=" item_text " style="margin-left:12em">
-Convert two arcs to one edge using maximum.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#mul</div></div>
-<div class=" item_text " style="margin-left:12em">
-Convert two arcs to one edge using multiplication.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#rev</div></div>
-<div class=" item_text " style="margin-left:12em">
-Encode graph in reverse direction.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#tp</div></div>
-<div class=" item_text " style="margin-left:12em">
-Same as above in matrix speak (<i>t</i>rans<i>p</i>ose).
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#selfrm</div></div>
-<div class=" item_text " style="margin-left:12em">
-Remove loops.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#selfmax</div></div>
-<div class=" item_text " style="margin-left:12em">
-Set loop value to maximum value.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#tug</div></div>
-<div class=" item_text " style="margin-left:12em">
-Perturb edge weights with factor arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#shrug</div></div>
-<div class=" item_text " style="margin-left:12em">
-Randomly perturb edge weights with factor arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#step</div></div>
-<div class=" item_text " style="margin-left:12em">
-Use the k-step relation, where <tt>k=arg</tt>.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#thread</div></div>
-<div class=" item_text " style="margin-left:12em">
-Set thread pool size to arg.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#arcmax</div></div>
-<div class=" item_text " style="margin-left:12em">
-Only keep largest arc between two nodes.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#arcsub</div></div>
-<div class=" item_text " style="margin-left:12em">
-Replace G by G - G^T.
-</div>
-<div class=" item_compact"><div class=" item_leftalign nowrap " >#symmcl</div></div>
-<div class=" item_text " style="margin-left:12em">
-As <tt>#mcl</tt>, use symmetrised graph for clustering.
-</div>
-</div>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-<a class="local sibling" href="mcl.html">mcl</a> accepts <b>--abc-neg-log</b> and <b>--abc-neg-log10</b>
-to specify log transformations. Similarly, <a class="local sibling" href="mcxload.html">mcxload</a> accepts
-<b>--stream-log</b>, <b>--stream-neg-log</b>, and
-<b>--stream-neg-log10</b>. The reason is that probabilities are sometimes
-encoded below the precision dictated by the IEEE (32 bit) float
-specification. This poses a problem as the mcl applications encode values
-by default as floats, and the transformation specifications are always
-applied to the mcl encoding. The options just mentioned are applied after a
-value has been read from an input stream and <i>before</i> it is converted to
-the native encoding.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcxassemble.html">mcxassemble</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Stijn van Dongen.</p>
-</body>
-</html>
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diff --git a/doc/mcxload.1 b/doc/mcxload.1
deleted file mode 100644
index fc4051a..0000000
--- a/doc/mcxload.1
+++ /dev/null
@@ -1,583 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxload" 1 "16 May 2014" "mcxload 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxload \- load matrices and tab files from label format
-.SH SYNOPSIS
-
-\fBmcxload\fP \fB-abc\fP <fname> (\fIlabel file\fP)
-\fB-o\fP <fname> (\fIoutput file\fP)
-
-\fB[-abc\fP <fname> (\fIlabel file\fP)\fB]\fP
-\fB[-123\fP <fname> (\fIidentifier file\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file\fP)\fB]\fP
-\fB[--stream-mirror\fP (\fIsymmetrify, same domain\fP)\fB]\fP
-\fB[--stream-split\fP (\fIassume different domains\fP)\fB]\fP
-\fB[-re\fP <mode> (\fIedge deduplication mode\fP)\fB]\fP
-\fB[-ri\fP <mode> (\fIimage symmetrification mode\fP)\fB]\fP
-\fB[-sif\fP <fname> (\fISIF label file\fP)\fB]\fP
-\fB[-etc\fP <fname> (\fI\&'etc\&' label file\fP)\fB]\fP
-\fB[-etc-ai\fP <fname> (\fIleaderless \&'etc\&' label file\fP)\fB]\fP
-\fB[--expect-values\fP (\fIexpect label:weight format\fP)\fB]\fP
-\fB[-235\fP <fname> (\fIleader \&'235\&' label file\fP)\fB]\fP
-\fB[-235-ai\fP <fname> (\fIleaderless \&'235\&' label file\fP)\fB]\fP
-\fB[-packed\fP <fname> (\fIfile/stream in binary format\fP)\fB]\fP
-\fB[-pack-cnum\fP <num> (\fIset column range\fP)\fB]\fP
-\fB[-pack-rnum\fP <num> (\fIset row range\fP)\fB]\fP
-\fB[-123-max\fP <int> (\fIset domain range\fP)\fB]\fP
-\fB[-123-maxc\fP <int> (\fIset column range\fP)\fB]\fP
-\fB[-123-maxr\fP <int> (\fIset row range\fP)\fB]\fP
-\fB[-write-tab\fP <fname> (\fIsave domain tab\fP)\fB]\fP
-\fB[-write-tabc\fP <fname> (\fIsave column tab\fP)\fB]\fP
-\fB[-write-tabr\fP <fname> (\fIsave row tab\fP)\fB]\fP
-\fB[-strict-tab\fP <fname> (\fItab universe\fP)\fB]\fP
-\fB[-strict-tabc\fP <fname> (\fItabc universe\fP)\fB]\fP
-\fB[-strict-tabr\fP <fname> (\fItabr universe\fP)\fB]\fP
-\fB[-restrict-tab\fP <fname> (\fItab world\fP)\fB]\fP
-\fB[-restrict-tabc\fP <fname> (\fItabc world\fP)\fB]\fP
-\fB[-restrict-tabr\fP <fname> (\fItabr world\fP)\fB]\fP
-\fB[-extend-tab\fP <fname> (\fItab launch\fP)\fB]\fP
-\fB[-extend-tabc\fP <fname> (\fItabc launch\fP)\fB]\fP
-\fB[-extend-tabr\fP <fname> (\fItabr launch\fP)\fB]\fP
-\fB[--stream-log\fP (\fIlog transform stream values\fP)\fB]\fP
-\fB[--stream-neg-log\fP (\fInegative log transform stream values\fP)\fB]\fP
-\fB[--stream-neg-log10\fP (\fInegative log-10 transform stream values\fP)\fB]\fP
-\fB[-stream-tf\fP (\fItransform stream values\fP)\fB]\fP
-\fB[-tf\fP <tf-spec> (\fItransform (not so) final matrix\fP)\fB]\fP
-\fB[--transpose\fP (\fItranspose\fP)\fB]\fP
-\fB[--write-binary\fP (\fIoutput binary format\fP)\fB]\fP
-\fB[--debug\fP (\fIdebug\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH GETTING STARTED
-
-.di ZV
-.in 0
-.nf \fC
- mcxload --stream-mirror -abc data1\&.txt -o data1\&.mci -write-tab data1\&.tab
- mcxload --stream-mirror -etc data2\&.txt -o data2\&.mci -write-tab data2\&.tab
- mcxload --stream-mirror -sif data3\&.txt -o data3\&.mci -write-tab data3\&.tab
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-When the output should be an undirected graph it is safest to always use
-the \fC--stream-mirror\fP option\&. Edges are stored bidirectionally as two arcs,
-and this option instructs \fBmcxload\fP to ensure that both arcs are present\&.
-In the above examples three different types of format are read\&. In all formats,
-the basic unit of specification is that of an arc specified by a source node,
-a destination node, and optionally a weight\&. All formats are line based,
-with \fB-abc\fP specifying a single arc and \fB-etc\fP and \fB-sif\fP
-specifying multiple arcs corresponding to a shared source node\&.
-For \fB-abc\fP the format is
-
-.di ZV
-.in 0
-.nf \fC
-<source-label> <destination-label> [<weight>]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-The last field, specifying the arc weight, is optional\&. If not present the arc weight will be
-set to the default weight of 1\&.0\&. For \fB-sif\fP the format is
-
-.di ZV
-.in 0
-.nf \fC
-<source-label> <relation-type> <destination-label> <destination-label> \&.\&.\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-There can be an arbitrary number of destination labels\&. The relation type field
-in the second column is required but will be ignored\&. As an extension it is possible
-to specify weights, requiring the use of the \fB--expect-values\fP option\&.
-Weights are specified by tagging them onto the destination label separated by a colon:
-
-.di ZV
-.in 0
-.nf \fC
-<source-label> <relation-type> <destination-label>:<weight> <destination-label>:<weight> \&.\&.\&.
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Finally, the format for the \fB-etc\fP option is the same, except that the relation type
-column is dropped\&.
-.SH DESCRIPTION
-\fBmcxload\fP reads label input from a file\&. The format of the file should be
-line-based, each line containing two white-space separated strings (labels)
-and optionally a number separated from the second label by whitespace\&. In
-the absence of a value, mcxload will use the default value 1\&.0\&. If a tab is
-present on an input line, mcxload will assume that the tab character is the
-separator for that line\&. Lines for which the first non-whitespace character
-is an octothorpe (\&'\fC#\fP\&') are skipped\&.
-
-\fBmcxload\fP will transform the labels into mcl numerical identifiers and the
-pairs of labels into graph edges or equivalently matrix entries\&. The weight
-of an edge is the value associated with the associated labels\&. mcxload
-constructs dictionaries (sometimes just one) that map labels onto mcl
-identifiers as it goes along\&. It can optionally write these to file\&. In MCL
-(family) parlance, such a dictionary written to file is called a \fItab
-file\fP\&.
-
-It is possible to specify numerical identifiers directly with
-the \fB-123\fP option\&. In this case \fBmcxload\fP assumes a canonical
-domain (cf \fBmcxio\fP) and will create the minimal canonical
-domain that supports the data\&. Also bear in mind the caveat further
-below\&.
-
-It is possible to effectively predeclare labels and thus enforce
-an a-priori known mapping of labels onto numerical identifiers\&.
-Labels receive an identifier in the order in which they occur
-in the input\&. Predeclaring labels can be achieved by
-having them appear in the desired order and setting the edge
-weight to zero\&.
-
-A major mcxload modality is whether the input refers to a single
-domain or to two separate domains\&. An example of the first is where
-labels are names of people and the value is the extent to which they
-like one another\&. This encodes a \fIlikability\fP graph where all
-the nodes represent people\&. The reasonable thing to do in this
-case is to create a single dictionary with all names wherever
-they occur\&. All \fBtab\fP options (as opposed to \fBtabc\fP and \fBtabr\fP)
-pertain to this scenario and likewise for the options \fB--graph\fP
-and \fB--stream-mirror\fP\&.
-
-An example of the second mode is where the first label is again the name of
-a person, the second label is the name of an animal species, and the value
-is the extent to which that person appreciates the species\&. In this case,
-the reasonable thing to do is to create two dictionaries, one for persons
-and one for species\&. All \fBtabc\fP and \fBtabr\fP options pertain to
-this scenario\&. The \fBtabc\fP options \fIalways refer to the first label\fP
-and the \fBtabr\fP options \fIalways refer to the second label\fP\&.
-The letters \fBc\fP and \fBr\fP refer to \fIcolumn\fP and \fIrow\fP respectively\&.
-The latter are the names of the matrix domains corresponding
-to the input domains\&. Refer to \fBmcxio(5)\fP\&.
-
-A further mcxload modality is whether it constructs dictionaries
-on the fly, or whether it proceeds from a tab file already
-available\&.
-By default mcxload will construct dictionaries on the fly\&. You
-need to save them with the appropriate \fB-write\fP option(s)\&.
-All the \fBstrict\fP options read a tab file
-and require any labels in the \fB-abc\fP\ \&\fIlabel input\fP
-to be present in the corresponding tab file\&. mcxload will then fail in
-the face of absent labels\&.
-All the \fBrestrict\fP options simply ignore labels that are
-not found in the corresponding tab file\&.
-The \fBextend\fP options extend the existing tab file with
-labels that are not found\&.
-It presumably only makes sense to do so if the corresponding
-\fB-write\fP options are used as well\&.
-
-The input stream is deduplicated on a per-node neighbourhood basis
-using the \fB-re\fP option\&.
-
-mcxload has a few options to transform or select based on
-the values in the input stream and the values in the
-constructed matrix\&. These are
-\fB--stream-log\fP,
-\fB--stream-neg-log\fP,
-\fB--stream-neg-log10\fP,
-\fB-stream-tf\fP and
-\fB-tf\fP\&.
-Refer to \fBmcxio(5)\fP for a description of the syntax accepted
-by the latter two options \- it is a syntax accepted
-by a few more mcl siblings\&.
-Finally it is possible to transpose the final result
-using the \fB--transpose\fP option\&. Keep in mind that
-mcxload does not accordingly change its idea of row and
-column domains\&.
-
-The final matrix can be symmetrified using the \fB-ri\fP option\&.
-
-The \fB-etc\fP, \fB-235\fP and \fB-sif\fP options
-assume a format where all entries for a given
-column (or equivalently all neighbours for a given node) are joined onto a
-single line\&. This can be useful e\&.g\&. to read in externally generated
-clusterings\&. The \fB-etc\fP and \fB-sif\fP options expect label
-input, whereas the \fB-235\fP options expects numbers in the input that
-are mapped directly onto mcl numerical identifiers\&.
-The SIF format expected by \fB-sif\fP requires a \fIrelationship type\fP
-in the second field on each line; this is ignored\&.
-As an extension to the SIF format
-weights may optionally follow the labels, separated from them with a colon character\&.
-
-\fBCAVEAT\fP
-.br
-Please note that by feeding the line \&'1000000000 1\&' to \fBmcxload\fP with either
-of the \fB-235\fP or \fB-123\fP options it will try to allocate a
-matrix with one billion columns\&. This is most likely not what is wanted\&.
-Assuming that the input contains fewer than one billion unique labels, one
-should use the label options as described above and below\&.
-
-\fBSTAGES\fP
-.br
-Conceptually, input matrix creation consists of the following stages
-
-.ZJ 2m 2m "i"
-Read the input stream, apply \fB-stream-tf\fP transformation
-specification, and optionally push reverse elements
-(\fB--stream-mirror\fP)\&.
-.in -4m
-.ZJ 2m 2m "ii"
-Deduplicate edges in the context of all edges/arcs originating from
-a given node according to the \fB-re\fP option\&.
-.in -4m
-.ZJ 2m 2m "iii"
-Apply transpose symmetrification according to the
-\fB-ri\fP option, if used\&.
-.in -4m
-.ZJ 2m 2m "iv"
-Apply \fB-tf\fP transformation specification\&.
-.in -4m
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel file\fP)"
-\&
-.br
-The file to read label data from\&. Labels are separated by white-space\&. The
-labels may optionally be followed by a value (again separated by
-white-space), which is taken as the edge weight between the nodes
-corresponding with the labels\&. If a tab is present on an input line it is
-presumed to be the separator for that line, including the value if present\&.
-Lines for which the first non-blank character is the octothorpe (\&'\fC#\fP\&')
-are skipped\&.
-.in -2m
-
-.ZI 2m "\fB-123\fP <fname> (\fIidentifier file\fP)"
-\&
-.br
-The file to read numerical data from\&. The format is the same as
-for label data, but the identifiers are directly mapped onto mcl identifiers
-as described earlier\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file\fP)"
-\&
-.br
-The output file where the constructed matrix is written\&.
-.in -2m
-
-.ZI 2m "\fB--stream-mirror\fP (\fIsymmetrify, same domain\fP)"
-\&
-.br
-Whenever \fIlabel1\fP \fIlabel2\fP \fIvalue\fP
-is encountered in the input, mcxload inserts
-\fIlabel2\fP \fIlabel1\fP \fIvalue\fP in the input
-stream as well\&. This option implies that both labels
-belong to the same domain\&.
-.in -2m
-
-.ZI 2m "\fB--stream-split\fP (\fIassume different domains\fP)"
-\&
-.br
-This tells mcxload that the two labels belong to different domains\&.
-The program will create two tab files, one for columns and one
-for rows\&. This can be used for example to create a logical mapping of
-gene identifiers to species identifiers\&.
-.in -2m
-
-.ZI 2m "\fB-re\fP <max|add|mul|first|last> (\fIdeduplication mode\fP)"
-\&
-.br
-This specifies how mcxload should collapse repeated entries, that is edges
-for which a value is specified multiple times\&. This is done relative to a
-single node at a time, taking into account all neighbours assembled from the
-input stream\&. Note that \fB--stream-mirror\fP will result in
-duplicated entries if the input contains edge specifications in both ways\&.
-Also note that \fBfirst\fP and \fBlast\fP might not result in
-symmetric input if only \fB--stream-mirror\fP is used\&.
-.in -2m
-
-.ZI 2m "\fB-write-tab\fP <fname> (\fIsave domain tab\fP)"
-\&
-.br
-Write the domain to file\&. It applies to both label types\&.
-.in -2m
-
-.ZI 2m "\fB-write-tabc\fP <fname> (\fIsave column tab\fP)"
-\&
-.br
-Write the column domain to file\&. It applies to the first label found
-on each input line\&.
-.in -2m
-
-.ZI 2m "\fB-write-tabr\fP <fname> (\fIsave row tab\fP)"
-\&
-.br
-Write the column domain to file\&. It applies to the second label found
-on each input line\&.
-.in -2m
-
-.ZI 2m "\fB-strict-tab\fP <fname> (\fItab universe\fP)"
-\&
-.br
-Read a dictionary from file and require each label to be present in the
-dictionary\&. mcxload will exit on absentees\&.
-.in -2m
-
-.ZI 2m "\fB-strict-tabc\fP <fname> (\fItabc universe\fP)"
-\&
-.br
-Read a dictionary from file and require the first label on each line
-to be present in the dictionary\&. mcxload will exit on absentees\&.
-.in -2m
-
-.ZI 2m "\fB-strict-tabr\fP <fname> (\fItabr universe\fP)"
-\&
-.br
-Read a dictionary from file and require the second label on each line
-to be present in the dictionary\&. mcxload will exit on absentees\&.
-.in -2m
-
-.ZI 2m "\fB-restrict-tab\fP <fname> (\fItab world\fP)"
-\&
-.br
-Read a dictionary from file and only accept input lines (edges)
-for which both labels are present in the dictionary\&.
-mcxload will ignore absentees\&.
-.in -2m
-
-.ZI 2m "\fB-restrict-tabc\fP <fname> (\fItabc world\fP)"
-\&
-.br
-Read a dictionary from file and ignore input lines
-for which the first label is absent from the dictionary\&.
-.in -2m
-
-.ZI 2m "\fB-restrict-tabr\fP <fname> (\fItabr world\fP)"
-\&
-.br
-Read a dictionary from file and ignore input lines
-for which the second label is absent from the dictionary\&.
-.in -2m
-
-.ZI 2m "\fB-extend-tab\fP <fname> (\fItab launch\fP)"
-\&
-.br
-Read a dictionary from file and extend it with any
-label from the input not yet present in the dictionary\&.
-.in -2m
-
-.ZI 2m "\fB-extend-tabc\fP <fname> (\fItabc launch\fP)"
-\&
-.br
-Read a dictionary from file and extend it with all
-first labels from the input not yet present in the dictionary\&.
-.in -2m
-
-.ZI 2m "\fB-extend-tabr\fP <fname> (\fItabr launch\fP)"
-\&
-.br
-Read a dictionary from file and extend it with all
-second labels from the input not yet present in the dictionary\&.
-.in -2m
-
-.ZI 2m "\fB-123-max\fP <int> (\fIset domain range\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-123-maxc\fP <int> (\fIset column range\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-123-maxr\fP <int> (\fIset row range\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options limit the domain ranges accepted by the \fB-123\fP option\&.
-Numbers starting from \fI<int>\fP will be ignored, and the domain(s)
-will range from zero up to one less than \fI<int>\fP\&.
-The first, \fB-123-max\fP governs both domains, and \fB-123-maxc\fP
-and \fB-123-maxr\fP respectively govern the column and row domain\&.
-.in -2m
-
-.ZI 2m "\fB--stream-log\fP (\fIlog transform stream values\fP)"
-\&
-.br
-Replace each entry by its natural logarithm\&.
-.in -2m
-
-.ZI 2m "\fB--stream-neg-log\fP (\fInegative log transform stream values\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--stream-neg-log10\fP (\fInegative log-10 transform stream values\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Replace each entry by the negative of its natural logarithm and
-log-10 representation, respectively\&.
-This is for example useful to convert scores that denote probabilities
-or p-values such as BLAST scores\&.
-.in -2m
-
-.ZI 2m "\fB-stream-tf\fP (\fItransform stream values\fP)"
-\&
-.br
-Transform the stream values as they are read in according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform (not so) final matrix\fP)"
-\&
-.br
-Transform the matrix values after deduplication and symmetrification
-according to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-ri\fP (\fI<max|add|mul>\fP)"
-\&
-.br
-After the initial matrix has been assembled, it can be symmetrified by
-either of these options\&. They indicate the operation used to combine the
-entries of the transposed matrix and the original matrix\&. \fBmul\fP
-is special in that it treats missing entries (which are normally considered
-zero in mcl matrix operations) as one\&.
-.in -2m
-
-.ZI 2m "\fB--transpose\fP (\fItranspose\fP)"
-\&
-.br
-Write the transposed matrix to file\&. This is obviously not useful
-when a symmetric matrix has been generated\&.
-.in -2m
-
-.ZI 2m "\fB-etc\fP <fname> (\fI\&'etc\&' label file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-etc-ai\fP <fname> (\fIleaderless \&'etc\&' label file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-235\fP <fname> (\fI\&'235\&' label file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-235-ai\fP <fname> (\fIleaderless \&'235\&' label file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-sif\fP <fname> (\fISIF label file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--expect-values\fP (\fIexpect label:weight format\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The input is read in lines; each line is split on whitespace into labels\&.
-For \fB-etc\fP the first label is interpreted as the source node\&. All
-other labels are interpreted as destination nodes\&.
-Weights may optionally follow the labels, separated from them with a colon character\&.
-It is in this case necessary to use the \fB--expect-values\fP option\&.
-The SIF (Simple Interaction File) format expected by \fB-sif\fP is
-similar except that it contains an additional field\&. In this format the
-second column denotes the \fIrelationship type\fP\&. It is ignored by \fBmcxload\fP\&.
-For \fB-etc-ai\fP (\fIauto-increment\fP) all labels are interpreted as
-destination nodes and mcxload automatically creates a source node for each
-line it reads\&. This option can be useful to read in files encoding a
-clustering, where each line represents a cluster of white-space separated
-labels\&.
-
-The \fB-235\fP options are similar except that the input is not
-interpreted as labels but must consist of numbers that explicitly
-specify the matrix to be built\&.
-.in -2m
-
-.ZI 2m "\fB-packed\fP <fname> (\fIfile/stream in binary format\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-pack-cnum\fP <num> (\fIset column range\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-pack-rnum\fP <num> (\fIset row range\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The \fB-packed\fP option allows to read machine-readable data
-directly\&. The data has to correspond to the data types for indexes
-and values with with MCL was compiled\&. The use of \fB-pack-cnum\fP
-and \fB-pack-rnum\fP is required to set the limits of
-the ranges of indices that will be read\&.
-
-The \fC/scripts\fP directory of the MCL software contains scripts
-\fCpacked-example\&.sh\fP and \fCpacked-example2\&.sh\fP\&. The first shows the simple
-binary format that is accepted by \fB-packed\fP\&. It also documents the
-required include files and library and the method by which they can be
-referenced and linked to\&. The second expands on the first example by
-multiplexing binary output onto multiple output streams\&. Each output stream
-is read and loaded by an independent \fImcxload\fP instance\&. The final result
-is obtained by summing the individual matrices\&. This can be used to speed up
-the loading of large data by parallelisation\&.
-.in -2m
-
-.ZI 2m "\fB--write-binary\fP (\fIoutput binary format\fP)"
-\&
-.br
-The output matrix is written in native binary format \- refer to
-\fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB--debug\fP (\fIdebug\fP)"
-\&
-.br
-Among other things, this turns on warnings when \fBrestrict\fP tab
-files are used and labels are found to be missing\&.
-.in -2m
-.SH AUTHOR
-Stijn van Dongen\&.
-.SH SEE ALSO
-\fBmcxio(5)\fP,
-\fBmcxdump(1)\fP,
-\fBmcl(1)\fP,
-\fBmclfaq(7)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxload.html b/doc/mcxload.html
deleted file mode 100644
index 3d6ae93..0000000
--- a/doc/mcxload.html
+++ /dev/null
@@ -1,589 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-<title>The mcxload manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxload.ps"><b>mcxload</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#started">GETTING STARTED</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxload — load matrices and tab files from label format</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxload</b> <a class="intern" href="#opt-abc"><b>-abc</b> <fname> (<i>label file</i>)</a>
-<a class="intern" href="#opt-o"><b>-o</b> <fname> (<i>output file</i>)</a></p>
-<p style="margin-bottom:0" class="asd_par">
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>label file</i>)<b>]</b></a>
-<a class="intern" href="#opt-123"><b>[-123</b> <fname> (<i>identifier file</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file</i>)<b>]</b></a>
-<a class="intern" href="#opt--stream-mirror"><b>[--stream-mirror</b> (<i>symmetrify, same domain</i>)<b>]</b></a>
-<a class="intern" href="#opt--stream-split"><b>[--stream-split</b> (<i>assume different domains</i>)<b>]</b></a>
-<a class="intern" href="#opt-re"><b>[-re</b> <mode> (<i>edge deduplication mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-ri"><b>[-ri</b> <mode> (<i>image symmetrification mode</i>)<b>]</b></a>
-<a class="intern" href="#opt-sif"><b>[-sif</b> <fname> (<i>SIF label file</i>)<b>]</b></a>
-<a class="intern" href="#opt-etc"><b>[-etc</b> <fname> (<i>'etc' label file</i>)<b>]</b></a>
-<a class="intern" href="#opt-etc-ai"><b>[-etc-ai</b> <fname> (<i>leaderless 'etc' label file</i>)<b>]</b></a>
-<a class="intern" href="#opt--expect-values"><b>[--expect-values</b> (<i>expect label:weight format</i>)<b>]</b></a>
-<a class="intern" href="#opt-235"><b>[-235</b> <fname> (<i>leader '235' label file</i>)<b>]</b></a>
-<a class="intern" href="#opt-235-ai"><b>[-235-ai</b> <fname> (<i>leaderless '235' label file</i>)<b>]</b></a>
-<a class="intern" href="#opt-packed"><b>[-packed</b> <fname> (<i>file/stream in binary format</i>)<b>]</b></a>
-<a class="intern" href="#opt-pack-cnum"><b>[-pack-cnum</b> <num> (<i>set column range</i>)<b>]</b></a>
-<a class="intern" href="#opt-pack-rnum"><b>[-pack-rnum</b> <num> (<i>set row range</i>)<b>]</b></a>
-<a class="intern" href="#opt-123-max"><b>[-123-max</b> <int> (<i>set domain range</i>)<b>]</b></a>
-<a class="intern" href="#opt-123-maxc"><b>[-123-maxc</b> <int> (<i>set column range</i>)<b>]</b></a>
-<a class="intern" href="#opt-123-maxr"><b>[-123-maxr</b> <int> (<i>set row range</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-tab"><b>[-write-tab</b> <fname> (<i>save domain tab</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-tabc"><b>[-write-tabc</b> <fname> (<i>save column tab</i>)<b>]</b></a>
-<a class="intern" href="#opt-write-tabr"><b>[-write-tabr</b> <fname> (<i>save row tab</i>)<b>]</b></a>
-<a class="intern" href="#opt-strict-tab"><b>[-strict-tab</b> <fname> (<i>tab universe</i>)<b>]</b></a>
-<a class="intern" href="#opt-strict-tabc"><b>[-strict-tabc</b> <fname> (<i>tabc universe</i>)<b>]</b></a>
-<a class="intern" href="#opt-strict-tabr"><b>[-strict-tabr</b> <fname> (<i>tabr universe</i>)<b>]</b></a>
-<a class="intern" href="#opt-restrict-tab"><b>[-restrict-tab</b> <fname> (<i>tab world</i>)<b>]</b></a>
-<a class="intern" href="#opt-restrict-tabc"><b>[-restrict-tabc</b> <fname> (<i>tabc world</i>)<b>]</b></a>
-<a class="intern" href="#opt-restrict-tabr"><b>[-restrict-tabr</b> <fname> (<i>tabr world</i>)<b>]</b></a>
-<a class="intern" href="#opt-extend-tab"><b>[-extend-tab</b> <fname> (<i>tab launch</i>)<b>]</b></a>
-<a class="intern" href="#opt-extend-tabc"><b>[-extend-tabc</b> <fname> (<i>tabc launch</i>)<b>]</b></a>
-<a class="intern" href="#opt-extend-tabr"><b>[-extend-tabr</b> <fname> (<i>tabr launch</i>)<b>]</b></a>
-<a class="intern" href="#opt--stream-log"><b>[--stream-log</b> (<i>log transform stream values</i>)<b>]</b></a>
-<a class="intern" href="#opt--stream-neg-log"><b>[--stream-neg-log</b> (<i>negative log transform stream values</i>)<b>]</b></a>
-<a class="intern" href="#opt--stream-neg-log10"><b>[--stream-neg-log10</b> (<i>negative log-10 transform stream values</i>)<b>]</b></a>
-<a class="intern" href="#opt-stream-tf"><b>[-stream-tf</b> (<i>transform stream values</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> <tf-spec> (<i>transform (not so) final matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--transpose"><b>[--transpose</b> (<i>transpose</i>)<b>]</b></a>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>output binary format</i>)<b>]</b></a>
-<a class="intern" href="#opt--debug"><b>[--debug</b> (<i>debug</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="started"></a>
-<h2>GETTING STARTED</h2>
-<div class="verbatim"> mcxload --stream-mirror -abc data1.txt -o data1.mci -write-tab data1.tab
- mcxload --stream-mirror -etc data2.txt -o data2.mci -write-tab data2.tab
- mcxload --stream-mirror -sif data3.txt -o data3.mci -write-tab data3.tab</div>
-<p style="margin-top:0em; margin-bottom:0em">
-When the output should be an undirected graph it is safest to always use
-the <tt>--stream-mirror</tt> option. Edges are stored bidirectionally as two arcs,
-and this option instructs <a class="local sibling" href="mcxload.html">mcxload</a> to ensure that both arcs are present.
-In the above examples three different types of format are read. In all formats,
-the basic unit of specification is that of an arc specified by a source node,
-a destination node, and optionally a weight. All formats are line based,
-with <b>-abc</b> specifying a single arc and <b>-etc</b> and <b>-sif</b>
-specifying multiple arcs corresponding to a shared source node.
-For <b>-abc</b> the format is</p>
-<div class="verbatim"><source-label> <destination-label> [<weight>]</div>
-<p style="margin-bottom:0" class="asd_par">
-The last field, specifying the arc weight, is optional. If not present the arc weight will be
-set to the default weight of 1.0.</p> For <b>-sif</b> the format is
-<div class="verbatim"><source-label> <relation-type> <destination-label> <destination-label> ...</div>
-<p style="margin-bottom:0" class="asd_par">
-There can be an arbitrary number of destination labels. The relation type field
-in the second column is required but will be ignored. As an extension it is possible
-to specify weights, requiring the use of the <b>--expect-values</b> option.
-Weights are specified by tagging them onto the destination label separated by a colon:</p>
-<div class="verbatim"><source-label> <relation-type> <destination-label>:<weight> <destination-label>:<weight> ...</div>
-<p style="margin-bottom:0" class="asd_par">
-Finally, the format for the <b>-etc</b> option is the same, except that the relation type
-column is dropped.</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mcxload</b> reads label input from a file. The format of the file should be
-line-based, each line containing two white-space separated strings (labels)
-and optionally a number separated from the second label by whitespace. In
-the absence of a value, mcxload will use the default value 1.0. If a tab is
-present on an input line, mcxload will assume that the tab character is the
-separator for that line. Lines for which the first non-whitespace character
-is an octothorpe ('<tt>#</tt>') are skipped.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxload</b> will transform the labels into mcl numerical identifiers and the
-pairs of labels into graph edges or equivalently matrix entries. The weight
-of an edge is the value associated with the associated labels. mcxload
-constructs dictionaries (sometimes just one) that map labels onto mcl
-identifiers as it goes along. It can optionally write these to file. In MCL
-(family) parlance, such a dictionary written to file is called a <i>tab
-file</i>.</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible to specify numerical identifiers directly with
-the <a class="intern" href="#opt-123"><b>-123</b></a> option. In this case <b>mcxload</b> assumes a canonical
-domain (cf <a class="local sibling" href="mcxio.html">mcxio</a>) and will create the minimal canonical
-domain that supports the data. Also bear in mind the caveat further
-below.</p>
-<p style="margin-bottom:0" class="asd_par">
-It is possible to effectively predeclare labels and thus enforce
-an a-priori known mapping of labels onto numerical identifiers.
-Labels receive an identifier in the order in which they occur
-in the input. Predeclaring labels can be achieved by
-having them appear in the desired order and setting the edge
-weight to zero.</p>
-<p style="margin-bottom:0" class="asd_par">
-A major mcxload modality is whether the input refers to a single
-domain or to two separate domains. An example of the first is where
-labels are names of people and the value is the extent to which they
-like one another. This encodes a <i>likability</i> graph where all
-the nodes represent people. The reasonable thing to do in this
-case is to create a single dictionary with all names wherever
-they occur. All <b>tab</b> options (as opposed to <b>tabc</b> and <b>tabr</b>)
-pertain to this scenario and likewise for the options <a class="intern" href="#opt--graph"><b>--graph</b></a>
-and <a class="intern" href="#opt--stream-mirror"><b>--stream-mirror</b></a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-An example of the second mode is where the first label is again the name of
-a person, the second label is the name of an animal species, and the value
-is the extent to which that person appreciates the species. In this case,
-the reasonable thing to do is to create two dictionaries, one for persons
-and one for species. All <b>tabc</b> and <b>tabr</b> options pertain to
-this scenario. The <b>tabc</b> options <i>always refer to the first label</i>
-and the <b>tabr</b> options <i>always refer to the second label</i>.
-The letters <b>c</b> and <b>r</b> refer to <i>column</i> and <i>row</i> respectively.
-The latter are the names of the matrix domains corresponding
-to the input domains. Refer to <a class="local sibling" href="mcxio.html">mcxio</a>.</p>
-<p style="margin-bottom:0" class="asd_par">
-A further mcxload modality is whether it constructs dictionaries
-on the fly, or whether it proceeds from a tab file already
-available.
-By default mcxload will construct dictionaries on the fly. You
-need to save them with the appropriate <b>-write</b> option(s).
-All the <b>strict</b> options read a tab file
-and require any labels in the <a class="intern" href="#opt-abc"><b>-abc</b> <i>label input</i></a>
-to be present in the corresponding tab file. mcxload will then fail in
-the face of absent labels.
-All the <b>restrict</b> options simply ignore labels that are
-not found in the corresponding tab file.
-The <b>extend</b> options extend the existing tab file with
-labels that are not found.
-It presumably only makes sense to do so if the corresponding
-<b>-write</b> options are used as well.</p>
-<p style="margin-bottom:0" class="asd_par">
-The input stream is deduplicated on a per-node neighbourhood basis
-using the <a class="intern" href="#opt-re"><b>-re</b></a> option.</p>
-<p style="margin-bottom:0" class="asd_par">
-mcxload has a few options to transform or select based on
-the values in the input stream and the values in the
-constructed matrix. These are
-<a class="intern" href="#opt--stream-log"><b>--stream-log</b></a>,
-<a class="intern" href="#opt--stream-neg-log"><b>--stream-neg-log</b></a>,
-<a class="intern" href="#opt--stream-neg-log10"><b>--stream-neg-log10</b></a>,
-<a class="intern" href="#opt-stream-tf"><b>-stream-tf</b></a> and
-<a class="intern" href="#opt-tf"><b>-tf</b></a>.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of the syntax accepted
-by the latter two options — it is a syntax accepted
-by a few more mcl siblings.
-Finally it is possible to transpose the final result
-using the <a class="intern" href="#opt--transpose"><b>--transpose</b></a> option. Keep in mind that
-mcxload does not accordingly change its idea of row and
-column domains.</p>
-<p style="margin-bottom:0" class="asd_par">
-The final matrix can be symmetrified using the <a class="intern" href="#opt-ri"><b>-ri</b></a> option.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <a class="intern" href="#opt-etc"><b>-etc</b>, <b>-235</b></a> and <b>-sif</b> options
-assume a format where all entries for a given
-column (or equivalently all neighbours for a given node) are joined onto a
-single line. This can be useful e.g. to read in externally generated
-clusterings. The <b>-etc</b> and <b>-sif</b> options expect label
-input, whereas the <b>-235</b> options expects numbers in the input that
-are mapped directly onto mcl numerical identifiers.
-The <span class="smallcaps">SIF</span> format expected by <b>-sif</b> requires a <i>relationship type</i>
-in the second field on each line; this is ignored.
-As an extension to the <span class="smallcaps">SIF</span> format
-weights may optionally follow the labels, separated from them with a colon character.
-</p>
-<p style="margin-bottom:0"><b>CAVEAT</b><br>
-Please note that by feeding the line '1000000000 1' to <b>mcxload</b> with either
-of the <b>-235</b> or <b>-123</b> options it will try to allocate a
-matrix with one billion columns. This is most likely not what is wanted.
-Assuming that the input contains fewer than one billion unique labels, one
-should use the label options as described above and below.
-</p>
-<p style="margin-bottom:0"><b>STAGES</b><br>
-Conceptually, input matrix creation consists of the following stages</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign " style="right:-2em">i</div></div>
-<div class=" item_text " style="margin-left:4em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read the input stream, apply <a class="intern" href="#opt-stream-tf"><b>-stream-tf</b></a> transformation
-specification, and optionally push reverse elements
-(<a class="intern" href="#opt--stream-mirror"><b>--stream-mirror</b></a>).</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-2em">ii</div></div>
-<div class=" item_text " style="margin-left:4em">
-<p style="margin-top:0em; margin-bottom:0em">
-Deduplicate edges in the context of all edges/arcs originating from
-a given node according to the <a class="intern" href="#opt-re"><b>-re</b></a> option.</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-2em">iii</div></div>
-<div class=" item_text " style="margin-left:4em">
-<p style="margin-top:0em; margin-bottom:0em">
-Apply transpose symmetrification according to the
-<a class="intern" href="#opt-ri"><b>-ri</b></a> option, if used.</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-2em">iv</div></div>
-<div class=" item_text " style="margin-left:4em">
-<p style="margin-top:0em; margin-bottom:0em">
-Apply <a class="intern" href="#opt-tf"><b>-tf</b></a> transformation specification.</p>
-</div>
-</div>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file to read label data from. Labels are separated by white-space. The
-labels may optionally be followed by a value (again separated by
-white-space), which is taken as the edge weight between the nodes
-corresponding with the labels. If a tab is present on an input line it is
-presumed to be the separator for that line, including the value if present.
-Lines for which the first non-blank character is the octothorpe ('<tt>#</tt>')
-are skipped.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-123"></a><b>-123</b> <fname> (<i>identifier file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file to read numerical data from. The format is the same as
-for label data, but the identifiers are directly mapped onto mcl identifiers
-as described earlier.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">The output file where the constructed matrix is written.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--stream-mirror"></a><b>--stream-mirror</b> (<i>symmetrify, same domain</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Whenever <i>label1</i> <i>label2</i> <i>value</i>
-is encountered in the input, mcxload inserts
-<i>label2</i> <i>label1</i> <i>value</i> in the input
-stream as well. This option implies that both labels
-belong to the same domain.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--stream-split"></a><b>--stream-split</b> (<i>assume different domains</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This tells mcxload that the two labels belong to different domains.
-The program will create two tab files, one for columns and one
-for rows. This can be used for example to create a logical mapping of
-gene identifiers to species identifiers.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-re"></a><b>-re</b> <max|add|mul|first|last> (<i>deduplication mode</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This specifies how mcxload should collapse repeated entries, that is edges
-for which a value is specified multiple times. This is done relative to a
-single node at a time, taking into account all neighbours assembled from the
-input stream. Note that <a class="intern" href="#opt--stream-mirror"><b>--stream-mirror</b></a> will result in
-duplicated entries if the input contains edge specifications in both ways.
-Also note that <b>first</b> and <b>last</b> might not result in
-symmetric input if only <b>--stream-mirror</b> is used.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-tab"></a><b>-write-tab</b> <fname> (<i>save domain tab</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the domain to file. It applies to both label types.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-tabc"></a><b>-write-tabc</b> <fname> (<i>save column tab</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the column domain to file. It applies to the first label found
-on each input line.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-write-tabr"></a><b>-write-tabr</b> <fname> (<i>save row tab</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the column domain to file. It applies to the second label found
-on each input line.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-strict-tab"></a><b>-strict-tab</b> <fname> (<i>tab universe</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and require each label to be present in the
-dictionary. mcxload will exit on absentees.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-strict-tabc"></a><b>-strict-tabc</b> <fname> (<i>tabc universe</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and require the first label on each line
-to be present in the dictionary. mcxload will exit on absentees.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-strict-tabr"></a><b>-strict-tabr</b> <fname> (<i>tabr universe</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and require the second label on each line
-to be present in the dictionary. mcxload will exit on absentees.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-restrict-tab"></a><b>-restrict-tab</b> <fname> (<i>tab world</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and only accept input lines (edges)
-for which both labels are present in the dictionary.
-mcxload will ignore absentees.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-restrict-tabc"></a><b>-restrict-tabc</b> <fname> (<i>tabc world</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and ignore input lines
-for which the first label is absent from the dictionary.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-restrict-tabr"></a><b>-restrict-tabr</b> <fname> (<i>tabr world</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and ignore input lines
-for which the second label is absent from the dictionary.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-extend-tab"></a><b>-extend-tab</b> <fname> (<i>tab launch</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and extend it with any
-label from the input not yet present in the dictionary.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-extend-tabc"></a><b>-extend-tabc</b> <fname> (<i>tabc launch</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and extend it with all
-first labels from the input not yet present in the dictionary.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-extend-tabr"></a><b>-extend-tabr</b> <fname> (<i>tabr launch</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a dictionary from file and extend it with all
-second labels from the input not yet present in the dictionary.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-123-max"></a><b>-123-max</b> <int> (<i>set domain range</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-123-maxc"></a><b>-123-maxc</b> <int> (<i>set column range</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-123-maxr"></a><b>-123-maxr</b> <int> (<i>set row range</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options limit the domain ranges accepted by the <b>-123</b> option.
-Numbers starting from <i><int></i> will be ignored, and the domain(s)
-will range from zero up to one less than <i><int></i>.
-The first, <b>-123-max</b> governs both domains, and <b>-123-maxc</b>
-and <b>-123-maxr</b> respectively govern the column and row domain.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--stream-log"></a><b>--stream-log</b> (<i>log transform stream values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Replace each entry by its natural logarithm.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--stream-neg-log"></a><b>--stream-neg-log</b> (<i>negative log transform stream values</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--stream-neg-log10"></a><b>--stream-neg-log10</b> (<i>negative log-10 transform stream values</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Replace each entry by the negative of its natural logarithm and
-log-10 representation, respectively.
-This is for example useful to convert scores that denote probabilities
-or p-values such as BLAST scores.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-stream-tf"></a><b>-stream-tf</b> (<i>transform stream values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the stream values as they are read in according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform (not so) final matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the matrix values after deduplication and symmetrification
-according to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-ri"></a><b>-ri</b> (<i><max|add|mul></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-After the initial matrix has been assembled, it can be symmetrified by
-either of these options. They indicate the operation used to combine the
-entries of the transposed matrix and the original matrix. <b>mul</b>
-is special in that it treats missing entries (which are normally considered
-zero in mcl matrix operations) as one.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--transpose"></a><b>--transpose</b> (<i>transpose</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the transposed matrix to file. This is obviously not useful
-when a symmetric matrix has been generated.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-etc"></a><b>-etc</b> <fname> (<i>'etc' label file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-etc-ai"></a><b>-etc-ai</b> <fname> (<i>leaderless 'etc' label file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-235"></a><b>-235</b> <fname> (<i>'235' label file</i>)</div><div class=" item_cascade item_leftalign nowrap" [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The input is read in lines; each line is split on whitespace into labels.
-For <b>-etc</b> the first label is interpreted as the source node. All
-other labels are interpreted as destination nodes.
-Weights may optionally follow the labels, separated from them with a colon character.
-It is in this case necessary to use the <b>--expect-values</b> option.
-The <span class="smallcaps">SIF</span> (Simple Interaction File) format expected by <b>-sif</b> is
-similar except that it contains an additional field. In this format the
-second column denotes the <i>relationship type</i>. It is ignored by <a class="local sibling" href="mcxload.html">mcxload</a>.
-For <b>-etc-ai</b> (<i>auto-increment</i>) all labels are interpreted as
-destination nodes and mcxload automatically creates a source node for each
-line it reads. This option can be useful to read in files encoding a
-clustering, where each line represents a cluster of white-space separated
-labels.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>-235</b> options are similar except that the input is not
-interpreted as labels but must consist of numbers that explicitly
-specify the matrix to be built.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-packed"></a><b>-packed</b> <fname> (<i>file/stream in binary format</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-pack-cnum"></a><b>-pack-cnum</b> <num> (<i>set column range</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-pack-rnum"></a><b>-pack-rnum</b> <num> (<i>set row range</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The <b>-packed</b> option allows to read machine-readable data
-directly. The data has to correspond to the data types for indexes
-and values with with MCL was compiled. The use of <b>-pack-cnum</b>
-and <b>-pack-rnum</b> is required to set the limits of
-the ranges of indices that will be read.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <tt>/scripts</tt> directory of the MCL software contains scripts
-<tt>packed-example.sh</tt> and <tt>packed-example2.sh</tt>. The first shows the simple
-binary format that is accepted by <b>-packed</b>. It also documents the
-required include files and library and the method by which they can be
-referenced and linked to. The second expands on the first example by
-multiplexing binary output onto multiple output streams. Each output stream
-is read and loaded by an independent <i>mcxload</i> instance. The final result
-is obtained by summing the individual matrices. This can be used to speed up
-the loading of large data by parallelisation.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--write-binary"></a><b>--write-binary</b> (<i>output binary format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The output matrix is written in native binary format — refer to
-<a class="local sibling" href="mcxio.html">mcxio</a>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--debug"></a><b>--debug</b> (<i>debug</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Among other things, this turns on warnings when <b>restrict</b> tab
-files are used and labels are found to be missing.</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Stijn van Dongen.</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-<a class="local sibling" href="mcxdump.html">mcxdump</a>,
-<a class="local sibling" href="mcl.html">mcl</a>,
-<a class="local sibling" href="mclfaq.html">mclfaq</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
diff --git a/doc/mcxload.ps b/doc/mcxload.ps
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diff --git a/doc/mcxmap.1 b/doc/mcxmap.1
deleted file mode 100644
index 8058426..0000000
--- a/doc/mcxmap.1
+++ /dev/null
@@ -1,223 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxmap" 1 "16 May 2014" "mcxmap 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxmap \- permute or remap the indices of graphs and matrices\&.
-.SH SYNOPSIS
-
-\fBmcxmap\fP
-\fB-imx\fP fname (\fIinput\fP)
-\fB[-o\fP fname (\fIoutput\fP)\fB]\fP
-\fB[-make-map\fP (\fIoutput map file name\fP)\fB]\fP
-\fB[-make-mapc\fP (\fIoutput map file name\fP)\fB]\fP
-\fB[-make-mapr\fP (\fIoutput map file name\fP)\fB]\fP
-\fB[-cmul\fP a (\fIcoefficient\fP)\fB]\fP
-\fB[-cshift\fP b (\fItranslate\fP)\fB]\fP
-\fB[-rmul\fP c (\fIcoefficient\fP)\fB]\fP
-\fB[-rshift\fP d (\fItranslate\fP)\fB]\fP
-\fB[-mul\fP e (\fIcoefficient\fP)\fB]\fP
-\fB[-shift\fP f (\fItranslate\fP)\fB]\fP
-\fB[-map\fP fname (\fIrow/col map file\fP)\fB]\fP
-\fB[-rmap\fP fname (\fIrow map file\fP)\fB]\fP
-\fB[-cmap\fP fname (\fIcolumn map file\fP)\fB]\fP
-\fB[-mapi\fP fname (\fIrow/col map file (use inverse)\fP)\fB]\fP
-\fB[-rmapi\fP fname (\fIrow map file (use inverse)\fP)\fB]\fP
-\fB[-cmapi\fP fname (\fIcolumn map file (use inverse)\fP)\fB]\fP
-\fB[-tab\fP fname (\fIread (and map) tab file\fP)\fB]\fP
-.SH DESCRIPTION
-
-This utility relabels graphs or matrices\&. Its main use is in applying a
-\fImap file\fP to a given matrix or graph\&. A map file contains a so called
-\fImap matrix\fP in mcl format that has some special properties (given
-further below)\&. The functionality of mcxmap can also be provided by \fBmcx\fP, as
-a mapped matrix (i\&.e\&. the result of applying a map matrix to another matrix)
-is simply the usual matrix product of a matrix and a map matrix\&. However,
-\fBmcx\fP will construct a new matrix and leave the original matrix to be mapped
-alone\&. When dealing with huge matrices, considerable gains in efficiency
-memory-wise and time-wise can be achieved by doing the mapping in-place\&.
-This is what mcxmap does\&. In the future, its functionality may be
-embedded in \fBmcx\fP with new mcx operators\&.
-
-The special properties of a map matrix are
-
-.ZJ 1m 1m "\(bu"
-The column domain and row domain are
-of the same cardinality\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Each column has exactly one entry\&.
-.in -2m
-.ZJ 1m 1m "\(bu"
-Each row domain index occurs in exactly one column\&.
-.in -2m
-
-These properties imply that the matrix can be used
-as a map from the column domain onto the row domain\&.
-An example map matrix is found in the \fBEXAMPLES\fP Section\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
-\&
-.br
-Output file\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP fname (\fIinput file\fP)"
-\&
-.br
-Input file\&.
-.in -2m
-
-.ZI 2m "\fB-map\fP fname (\fIrow/col map file)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-rmap\fP fname (\fIrow map file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cmap\fP fname (\fIcolumn map file\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-mapi\fP fname (\fIrow/col map file (use inverse)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-rmapi\fP fname (\fIrow map fil (use inverse)\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cmapi\fP fname (\fIcolumn map fil (use inverse)\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Different ways to specify map files\&.
-.in -2m
-
-.ZI 2m "\fB-make-map\fP (\fIoutput map file name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-make-mapc\fP (\fIoutput map file name\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-make-mapr\fP (\fIoutput map file name\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Generate a map that maps the specified domain onto
-the appropriate canonical domain and write the map
-matrix to file\&.
-.in -2m
-
-.ZI 2m "\fB-cmul\fP a (\fIcoefficient\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-cshift\fP b (\fItranslate\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options have affect if neither a column map file nor column
-canonification is specified\&. If any of the first two options is used,
-column indices\ \&\fCi\fP are mapped to\ \&\fCa*i+b\fP\&.
-.in -2m
-
-.ZI 2m "\fB-rmul\fP c (\fIcoefficient\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-rshift\fP d (\fItranslate\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options have affect if neither a row map file nor row
-canonification is specified\&. If any of the first two options is used,
-indices\ \&\fCi\fP are mapped to\ \&\fCc*i+d\fP\&.
-.in -2m
-
-.ZI 2m "\fB-mul\fP e (\fIcoefficient\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-shift\fP f (\fItranslate\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-If a map file is specified for a given domain, neither a map file nor
-canonification is specified\&. If any of the first two options is used, the
-indices\ \&\fCi\fP will be mapped to\ \&\fCe*i+f\fP\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP fname (\fIread (and map) tab file\fP)"
-\&
-.br
-This option requires the \fB-map\fP option\&. \fBmcxmap\fP will output the
-mapped tab definition\&.
-.in -2m
-.SH EXAMPLES
-
-The matrix below has two canonical domains which are identical\&.
-It denotes a map of the canonical domain onto itself, in which
-node 0 is relabeled to 8, node 1 is relabeled to 5, et cetera\&.
-
-.nf \fC
-(mclheader
-mcltype matrix
-dimensions 12x12
-)
-(mclmatrix
-begin
-0 8 $
-1 5 $
-2 3 $
-3 2 $
-4 4 $
-5 6 $
-6 7 $
-7 9 $
-8 1 $
-9 10 $
-10 11 $
-11 0 $
-)
-.fi \fR
-
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-\fBmcx(1)\fP,
-\fBmcxsubs(1)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxmap.html b/doc/mcxmap.html
deleted file mode 100644
index a098796..0000000
--- a/doc/mcxmap.html
+++ /dev/null
@@ -1,281 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
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-a:link { text-decoration: none; }
-a:active { text-decoration: none; }
-a:visited { text-decoration: none; }
-a:link { color: #1111aa; }
-a:active { color: #1111aa; }
-a:visited { color: #111166; }
-a.local:link { color: #11aa11; }
-a.local:active { color: #11aa11; }
-a.local:visited { color: #116611; }
-a.intern:link { color: #1111aa; }
-a.intern:active { color: #1111aa; }
-a.intern:visited { color: #111166; }
-a.extern:link { color: #aa1111; }
-a.extern:active { color: #aa1111; }
-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
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-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
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-.item_rightalign
-{ width: 2em;
-text-align: right;
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-{ position: absolute;
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-{ position: relative;
-margin-left: 3em;
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-.smallcaps { font-size: smaller; text-transform: uppercase }
-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
-margin-right: 8%;
-}
-</style>
-<title>The mcxmap manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxmap.ps"><b>mcxmap</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#examples">EXAMPLES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxmap — permute or remap the indices of graphs and matrices.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxmap</b>
-<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input</i>)</a></p>
-<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output</i>)<b>]</b></a>
-<a class="intern" href="#opt-make-map"><b>[-make-map</b> (<i>output map file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-make-mapc"><b>[-make-mapc</b> (<i>output map file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-make-mapr"><b>[-make-mapr</b> (<i>output map file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-cmul"><b>[-cmul</b> a (<i>coefficient</i>)<b>]</b></a>
-<a class="intern" href="#opt-cshift"><b>[-cshift</b> b (<i>translate</i>)<b>]</b></a>
-<a class="intern" href="#opt-rmul"><b>[-rmul</b> c (<i>coefficient</i>)<b>]</b></a>
-<a class="intern" href="#opt-rshift"><b>[-rshift</b> d (<i>translate</i>)<b>]</b></a>
-<a class="intern" href="#opt-mul"><b>[-mul</b> e (<i>coefficient</i>)<b>]</b></a>
-<a class="intern" href="#opt-shift"><b>[-shift</b> f (<i>translate</i>)<b>]</b></a>
-<a class="intern" href="#opt-map"><b>[-map</b> fname (<i>row/col map file</i>)<b>]</b></a>
-<a class="intern" href="#opt-rmap"><b>[-rmap</b> fname (<i>row map file</i>)<b>]</b></a>
-<a class="intern" href="#opt-cmap"><b>[-cmap</b> fname (<i>column map file</i>)<b>]</b></a>
-<a class="intern" href="#opt-mapi"><b>[-mapi</b> fname (<i>row/col map file (use inverse)</i>)<b>]</b></a>
-<a class="intern" href="#opt-rmapi"><b>[-rmapi</b> fname (<i>row map file (use inverse)</i>)<b>]</b></a>
-<a class="intern" href="#opt-cmapi"><b>[-cmapi</b> fname (<i>column map file (use inverse)</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> fname (<i>read (and map) tab file</i>)<b>]</b></a>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-This utility relabels graphs or matrices. Its main use is in applying a
-<i>map file</i> to a given matrix or graph. A map file contains a so called
-<i>map matrix</i> in mcl format that has some special properties (given
-further below). The functionality of mcxmap can also be provided by <b>mcx</b>, as
-a mapped matrix (i.e. the result of applying a map matrix to another matrix)
-is simply the usual matrix product of a matrix and a map matrix. However,
-<b>mcx</b> will construct a new matrix and leave the original matrix to be mapped
-alone. When dealing with huge matrices, considerable gains in efficiency
-memory-wise and time-wise can be achieved by doing the mapping in-place.
-This is what mcxmap does. In the future, its functionality may be
-embedded in <b>mcx</b> with new mcx operators.</p>
-<p style="margin-bottom:0" class="asd_par">
-The special properties of a map matrix are</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The column domain and row domain are
-of the same cardinality.</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Each column has exactly one entry.</p>
-</div>
-<div class=" item_compact"><div class=" item_rightalign " style="right:-1em"><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Each row domain index occurs in exactly one column.</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-These properties imply that the matrix can be used
-as a map from the column domain onto the row domain.
-An example map matrix is found in the <a class="intern" href="#examples">EXAMPLES</a> Section.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> fname (<i>input file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Input file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-map"></a><b>-map</b> fname (<i>row/col map file)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-rmap"></a><b>-rmap</b> fname (<i>row map file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cmap"></a><b>-cmap</b> fname (<i>column map file</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-mapi"></a><b>-mapi</b> fna [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Different ways to specify map files.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-make-map"></a><b>-make-map</b> (<i>output map file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-make-mapc"></a><b>-make-mapc</b> (<i>output map file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-make-mapr"></a><b>-make-mapr</b> (<i>output map file name</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Generate a map that maps the specified domain onto
-the appropriate canonical domain and write the map
-matrix to file.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cmul"></a><b>-cmul</b> a (<i>coefficient</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-cshift"></a><b>-cshift</b> b (<i>translate</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options have affect if neither a column map file nor column
-canonification is specified. If any of the first two options is used,
-column indices <tt>i</tt> are mapped to <tt>a*i+b</tt>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-rmul"></a><b>-rmul</b> c (<i>coefficient</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-rshift"></a><b>-rshift</b> d (<i>translate</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options have affect if neither a row map file nor row
-canonification is specified. If any of the first two options is used,
-indices <tt>i</tt> are mapped to <tt>c*i+d</tt>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-mul"></a><b>-mul</b> e (<i>coefficient</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-shift"></a><b>-shift</b> f (<i>translate</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If a map file is specified for a given domain, neither a map file nor
-canonification is specified. If any of the first two options is used, the
-indices <tt>i</tt> will be mapped to <tt>e*i+f</tt>.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> fname (<i>read (and map) tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option requires the <b>-map</b> option. <b>mcxmap</b> will output the
-mapped tab definition.
-</p>
-</div>
-</div>
-
-<a name="examples"></a>
-<h2>EXAMPLES</h2>
-<p style="margin-bottom:0" class="asd_par">
-The matrix below has two canonical domains which are identical.
-It denotes a map of the canonical domain onto itself, in which
-node 0 is relabeled to 8, node 1 is relabeled to 5, et cetera.
-</p>
-<div class="verbatim">(mclheader
-mcltype matrix
-dimensions 12x12
-)
-(mclmatrix
-begin
-0 8 $
-1 5 $
-2 3 $
-3 2 $
-4 4 $
-5 6 $
-6 7 $
-7 9 $
-8 1 $
-9 10 $
-10 11 $
-11 0 $
-)
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-<a class="local sibling" href="mcx.html">mcx</a>,
-<a class="local sibling" href="mcxsubs.html">mcxsubs</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
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diff --git a/doc/mcxquery.1 b/doc/mcxquery.1
deleted file mode 100644
index f1af8c5..0000000
--- a/doc/mcxquery.1
+++ /dev/null
@@ -1,309 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcx q" 1 "16 May 2014" "mcx q 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxquery \- compute simple graph statistics
-.SH SYNOPSIS
-
-mcxquery is not in actual fact a program\&. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode \fIquery\fP\&. The options \fB-h\fP, \fB--apropos\fP,
-\fB--version\fP, \fB-set\fP, \fB--nop\fP, \fB-progress\fP\ \&\fI<num>\fP
-are accessible
-in all \fBmcx\fP modes\&. They are described
-in the \fBmcx\fP manual page\&.
-
-\fBmcxquery\fP
-\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
-\fB[-imx\fP <fname> (\fIspecify matrix input\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput file name\fP)\fB]\fP
-\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
-\fB[--node-attr\fP (\fIoutput node degree and weight attributes\fP)\fB]\fP
-\fB[-vary-threshold\fP <start/end/step> (\fIanalyze graph at similarity cutoffs\fP)\fB]\fP
-\fB[-vary-knn\fP <start/end/step> (\fIanalyze graph for varying k-NN\fP)\fB]\fP
-\fB[-vary-ceil\fP <start/end/step> (\fIanalyze graph for varying ceil reductions\fP)\fB]\fP
-\fB[--no-legend\fP (\fIdo not output explanatory legend\fP)\fB]\fP
-\fB[--reduce\fP (\fIuse reduced matrix\fP)\fB]\fP
-\fB[--test-metric\fP (\fItest whether graph distance is metric\fP)\fB]\fP
-\fB[--test-cycle\fP (\fItest whether graph contains cycles\fP)\fB]\fP
-\fB[-test-cycle\fP <num> (\fItest cycles, report cycles\fP)\fB]\fP
-\fB[--vary-correlation\fP (\fIanalyze graph at correlation cutoffs\fP)\fB]\fP
-\fB[--clcf\fP (\fIinclude clustering coefficient analysis\fP)\fB]\fP
-\fB[--eff\fP (\fIinclude efficiency criterion\fP)\fB]\fP
-\fB[-div\fP <num> (\fIcluster size separating value\fP)\fB]\fP
-\fB[--dim\fP (\fIreport native format and dimensions\fP)\fB]\fP
-\fB[--values\fP (\fIoutput all arc entries/weights, unsorted\fP)\fB]\fP
-\fB[--values-sorted\fP (\fIoutput all entries/weights, sorted\fP)\fB]\fP
-\fB[-values-hist\fP <nbins|start/end/nbins> (\fIweight histogram\fP)\fB]\fP
-\fB[-degrees-hist\fP <step> (\fIdegrees histogram\fP)\fB]\fP
-\fB[--output-table\fP (\fIoutput logical tab separated table without key\fP)\fB]\fP
-\fB[-t\fP <num> (\fInumber of threads to use\fP)\fB]\fP
-\fB[-icl\fP <fname> (\fIinput clustering\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-The default \fBmcxquery\fP output is a list of summary statistics for each
-node\&. These are its node degree, the mean, minimum, maximum and median
-edge weight\&. If supplied with a clustering, the output will additionally
-list the cluster size and cluster label for each node\&.
-
-Additionally, \fBmcxquery\fP can be used to analyse a graph at different similarity
-cutoffs or at varying parameters of edge reduction strategies such as mutual
-nearest neighbour reduction\&.
-Attributes supplied across different thresholds are the number of connected
-components, the number of singletons, and statistics (median, average, iqr)
-on node degrees and edge weights\&.
-Typically this is done on a graph constructed using a very permissive
-threshold\&. For example, one can create a graph from array expression data
-using \fBmcxarray\fP with a very low pearson correlation cutoff such as\ \&0\&.5
-Then \fBmcxquery\fP can be used to analyze the graph at increasingly
-stringent thresholds of\ \&0\&.50, 0\&.55, 0\&.60\ \&\&.\&.\ \&0\&.95\&.
-
-Other tasks that \fBmcxquery\fP be used for include:
-
-.ZI 2m "\(bu"
-Produce a histogram of edge weights\&.
-.in -2m
-.ZI 2m "\(bu"
-Produce a histogram of edge node degrees\&.
-.in -2m
-.ZI 2m "\(bu"
-Output all edge weights\&.
-.in -2m
-.ZI 2m "\(bu"
-Test whether the graph weight encodes a metric
-(for edge weights that encode distances rather than similarites)\&.
-.in -2m
-.ZI 2m "\(bu"
-Test whether the graph has a cycle\&.
-.in -2m
-.SH OPTIONS
-
-.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
-\&
-.br
-The file name for input that is in label format\&.
-.in -2m
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input that is in mcl native matrix format\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput file name\fP)"
-\&
-.br
-Set the name of the file where output should be written to\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
-\&
-.br
-This option causes the output to be printed with the labels
-found in the tab file\&.
-.in -2m
-
-.ZI 2m "\fB--dim\fP (\fIreport native format and dimensions\fP)"
-\&
-.br
-This will report the matrix format (either interchange or binary)
-and the matrix dimensions\&. For a graph the two reported dimensions
-should be equal\&.
-.in -2m
-
-.ZI 2m "\fB--values\fP (\fIoutput all entries/weights, unsorted\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--values-sorted\fP (\fIoutput all entries/weights, sorted\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-values-hist\fP <start/end/nbins> (\fIoutput weight histogram\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-values-hist\fP <nbins> (\fIoutput weight histogram\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-degrees-hist\fP <nbins> (\fIdegrees histogram\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options are fairly self-documenting\&. The result of both
-\fB-edges-hist\fP and \fB-degrees-hist\fP
-is a tab separated table of bin offsets and bin counts\&.
-When using \fB-edges-hist\fP\ \&\fI<nbins>\fP the program will
-create a histogram ranging from the smallest to
-the largest edge weight\&.
-.in -2m
-
-.ZI 2m "\fB--output-table\fP (\fIoutput logical tab separated table without key\fP)"
-\&
-.br
-This option causes table output such as provided by \fB--vary-correlation\fP
-to be output in a logical tab-separated format rather than pretty-printed\&.
-.in -2m
-
-.ZI 2m "\fB-vary-threshold\fP <start/end/nbins> (\fIanalyze graphs at similarity cutoffs\fP)"
-\&
-.br
-The graph is analysed at different edge weight thresholds, going from \fB<start>\fP
-to \fB<end>\fP in \fB<nbins>\fP steps\&.
-.in -2m
-
-.ZI 2m "\fB--vary-correlation\fP (\fIanalyze graphs at correlation cutoffs\fP)"
-\&
-.br
-This instructs \fBmcxquery\fP to use a threshold list suitable for use with graphs
-in which the edge weight similarities are correlations\&.
-The list starts at 0\&.2 and ends at 1\&.0 using increments of 0\&.05\&.
-If a different start or increment is required it can
-be achieved by using the \fB-vary-threshold\fP option\&.
-For example, a start of\ \&0\&.10 and an increment of\ \&0\&.02 are obtained
-by issuing \fB-vary-threshold\fP\ \&\fB:\&.1/1\&.0/45\fP\&.
-.in -2m
-
-.ZI 2m "defopt{--no-legend}{do not output explanatory legend}"
-\&
-.br
-For a fully parseable output format use \fB--output-table\fP\&.
-.in -2m
-
-.ZI 2m "\fB--clcf\fP (\fIinclude clustering coefficient analysis\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--eff\fP (\fIinclude efficiency criterion\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options can be used to compute additional characteristics
-in the analysis of thresholded graphs with \fB--vary-correlation\fP
-and \fB-vary-threshold\fP\&. For large graphs these are relatively time-consuming
-to compute\&. More information and a reference for
-the efficiency criterion can be found in \fBclminfo(1)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-vary-knn\fP <start/end/step> (\fIanalyze graphs for varying k-NN\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-vary-ceil\fP <start/end/step> (\fIanalyze graphs for varying ceil reductions\fP)"
-\&
-'in -2m
-.ZI 2m "\fB--reduce\fP (\fIuse reduced matrix\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-These options cause analysis of a graph as it is subjected to reductions
-across a range of parameters\&. Refer to \fBmcxio(5)\fP for a description of
-these reductions\&. The analyses starts at the \fIend\fP argument, and
-progresses towards the \fIstart\fP argument using decrements of size
-\fIstep\fP\&. By default the reduction is always computed relative to the
-start matrix, i\&.e\&. the input matrix after \fB-tf\fP transformations have
-optionally been applied\&. Specifying \fB--reduce\fP causes this to change
-so that each new reduction is calculated relative to the reduction just
-computed\&.
-
-For graphs with ties among edge weights it may be useful to use
-\fB-tf\fP\ \&\fB\&'#tug()\&'\fP\&. This will add small perturbations to the
-edge weights and have the effect of breaking ties\&.
-By default perturbations are computed using the cosine between
-the vectors of neighbours of the two nodes incident to an edge\&.
-This can be changed to a random perturbation with
-\fB-tf\fP\ \&\fB\&'#rug()\&'\fP\&.
-.in -2m
-
-.ZI 2m "\fB--test-cycle\fP (\fItest whether graph contains cycles\fP)"
-\&
-'in -2m
-.ZI 2m "\fB-test-cycle\fP <num> (\fItest cycles, report cyclees\fP)"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Test whether the input graph contains cycles\&. With the second option
-nodes that are part of a cycle are output, up to a maximum of \fI<num>\fP
-nodes\&. Use \fI<num>\fP=\fB-1\fP to output all such nodes\&.
-.in -2m
-
-.ZI 2m "\fB--test-metric\fP (\fItest whether graph distance is metric\fP)"
-\&
-.br
-This tests all possible triangle relationships\&.
-.in -2m
-
-.ZI 2m "\fB-div\fP <num> (\fIcluster size separating value\fP)"
-\&
-.br
-When analyzing graphs at different thresholds with one of the
-options above, \fBmcxquery\fP reports the percentage of nodes contained
-in clusters not exceeding a specified size, by default\ \&3\&.
-This number can be changed using the \fB-div\fP option\&.
-.in -2m
-
-.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
-\&
-.br
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-t\fP <num> (\fInumber of threads to use\fP)"
-\&
-.br
-This has an effect only when using the \fB-vary-knn\fP option,
-and is only useful on multi-CPU machines\&.
-.in -2m
-
-.ZI 2m "\fB--node-attr\fP (\fIoutput node degree and weight attributes\fP)"
-\&
-.br
-Output is in the form of a tab separated file\&.
-The option \fB-icl\fP can be used in conjuction\&.
-.in -2m
-
-.ZI 2m "\fB-icl\fP <fname> (\fIinput clustering\fP)"
-\&
-.br
-Output for each node the size of the cluster it is in\&.
-This option can be used in conjunction with \fB--node-attr\fP\&.
-.in -2m
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
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-<title>The mcx q manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxquery.ps"><b>mcx q</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxquery — compute simple graph statistics</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">mcxquery is not in actual fact a program. This manual
-page documents the behaviour and options of the mcx program when
-invoked in mode <i>query</i>. The options <b>-h</b>, <b>--apropos</b>,
-<b>--version</b>, <b>-set</b>, <b>--nop</b>, <b>-progress</b> <i><num></i>
-are accessible
-in all <b>mcx</b> modes. They are described
-in the <a class="local sibling" href="mcx.html">mcx</a> manual page.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxquery</b>
-<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix input</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt--node-attr"><b>[--node-attr</b> (<i>output node degree and weight attributes</i>)<b>]</b></a>
-<a class="intern" href="#opt-vary-threshold"><b>[-vary-threshold</b> <start/end/step> (<i>analyze graph at similarity cutoffs</i>)<b>]</b></a>
-<a class="intern" href="#opt-vary-knn"><b>[-vary-knn</b> <start/end/step> (<i>analyze graph for varying k-NN</i>)<b>]</b></a>
-<a class="intern" href="#opt-vary-ceil"><b>[-vary-ceil</b> <start/end/step> (<i>analyze graph for varying ceil reductions</i>)<b>]</b></a>
-<a class="intern" href="#opt--no-legend"><b>[--no-legend</b> (<i>do not output explanatory legend</i>)<b>]</b></a>
-<a class="intern" href="#opt--reduce"><b>[--reduce</b> (<i>use reduced matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--test-metric"><b>[--test-metric</b> (<i>test whether graph distance is metric</i>)<b>]</b></a>
-<a class="intern" href="#opt--test-cycle"><b>[--test-cycle</b> (<i>test whether graph contains cycles</i>)<b>]</b></a>
-<a class="intern" href="#opt-test-cycle"><b>[-test-cycle</b> <num> (<i>test cycles, report cycles</i>)<b>]</b></a>
-<a class="intern" href="#opt--vary-correlation"><b>[--vary-correlation</b> (<i>analyze graph at correlation cutoffs</i>)<b>]</b></a>
-<a class="intern" href="#opt--clcf"><b>[--clcf</b> (<i>include clustering coefficient analysis</i>)<b>]</b></a>
-<a class="intern" href="#opt--eff"><b>[--eff</b> (<i>include efficiency criterion</i>)<b>]</b></a>
-<a class="intern" href="#opt-div"><b>[-div</b> <num> (<i>cluster size separating value</i>)<b>]</b></a>
-<a class="intern" href="#opt--dim"><b>[--dim</b> (<i>report native format and dimensions</i>)<b>]</b></a>
-<a class="intern" href="#opt--values"><b>[--values</b> (<i>output all arc entries/weights, unsorted</i>)<b>]</b></a>
-<a class="intern" href="#opt--values-sorted"><b>[--values-sorted</b> (<i>output all entries/weights, sorted</i>)<b>]</b></a>
-<a class="intern" href="#opt-values-hist"><b>[-values-hist</b> <nbins|start/end/nbins> (<i>weight histogram</i>)<b>]</b></a>
-<a class="intern" href="#opt-degrees-hist"><b>[-degrees-hist</b> <step> (<i>degrees histogram</i>)<b>]</b></a>
-<a class="intern" href="#opt--output-table"><b>[--output-table</b> (<i>output logical tab separated table without key</i>)<b>]</b></a>
-<a class="intern" href="#opt-t"><b>[-t</b> <num> (<i>number of threads to use</i>)<b>]</b></a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>input clustering</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-The default <b>mcxquery</b> output is a list of summary statistics for each
-node. These are its node degree, the mean, minimum, maximum and median
-edge weight. If supplied with a clustering, the output will additionally
-list the cluster size and cluster label for each node.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Additionally, <b>mcxquery</b> can be used to analyse a graph at different similarity
-cutoffs or at varying parameters of edge reduction strategies such as mutual
-nearest neighbour reduction.
-Attributes supplied across different thresholds are the number of connected
-components, the number of singletons, and statistics (median, average, iqr)
-on node degrees and edge weights.
-Typically this is done on a graph constructed using a very permissive
-threshold. For example, one can create a graph from array expression data
-using <b>mcxarray</b> with a very low pearson correlation cutoff such as 0.5
-Then <b>mcxquery</b> can be used to analyze the graph at increasingly
-stringent thresholds of 0.50, 0.55, 0.60 .. 0.95.
-</p>
-<p style="margin-bottom:0" class="asd_par">Other tasks that <b>mcxquery</b> be used for include:
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-Produce a histogram of edge weights.
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-Produce a histogram of edge node degrees.
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-Output all edge weights.
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-Test whether the graph weight encodes a metric
-(for edge weights that encode distances rather than similarites).
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-Test whether the graph has a cycle.
-</div>
-</div>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in label format.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input that is in mcl native matrix format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Set the name of the file where output should be written to.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes the output to be printed with the labels
-found in the tab file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--dim"></a><b>--dim</b> (<i>report native format and dimensions</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This will report the matrix format (either interchange or binary)
-and the matrix dimensions. For a graph the two reported dimensions
-should be equal.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--values"></a><b>--values</b> (<i>output all entries/weights, unsorted</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--values-sorted"></a><b>--values-sorted</b> (<i>output all entries/weights, sorted</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-values-hist"></a><b>-values-hist</b> <start/end/nbins> (<i>output weight histogram</i [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options are fairly self-documenting. The result of both
-<b>-edges-hist</b> and <b>-degrees-hist</b>
-is a tab separated table of bin offsets and bin counts.
-When using <b>-edges-hist</b> <i><nbins></i> the program will
-create a histogram ranging from the smallest to
-the largest edge weight.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--output-table"></a><b>--output-table</b> (<i>output logical tab separated table without key</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This option causes table output such as provided by <b>--vary-correlation</b>
-to be output in a logical tab-separated format rather than pretty-printed.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-vary-threshold"></a><b>-vary-threshold</b> <start/end/nbins> (<i>analyze graphs at similarity cutoffs</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The graph is analysed at different edge weight thresholds, going from <b><start></b>
-to <b><end></b> in <b><nbins></b> steps.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--vary-correlation"></a><b>--vary-correlation</b> (<i>analyze graphs at correlation cutoffs</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This instructs <b>mcxquery</b> to use a threshold list suitable for use with graphs
-in which the edge weight similarities are correlations.
-The list starts at 0.2 and ends at 1.0 using increments of 0.05.
-If a different start or increment is required it can
-be achieved by using the <b>-vary-threshold</b> option.
-For example, a start of 0.10 and an increment of 0.02 are obtained
-by issuing <b>-vary-threshold</b> <b>:.1/1.0/45</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >defopt{--no-legend}{do not output explanatory legend}</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-For a fully parseable output format use <a class="intern" href="#opt--output-table"><b>--output-table</b></a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--clcf"></a><b>--clcf</b> (<i>include clustering coefficient analysis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--eff"></a><b>--eff</b> (<i>include efficiency criterion</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options can be used to compute additional characteristics
-in the analysis of thresholded graphs with <b>--vary-correlation</b>
-and <b>-vary-threshold</b>. For large graphs these are relatively time-consuming
-to compute. More information and a reference for
-the efficiency criterion can be found in <a class="local sibling" href="clminfo.html">clminfo</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-vary-knn"></a><b>-vary-knn</b> <start/end/step> (<i>analyze graphs for varying k-NN</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-vary-ceil"></a><b>-vary-ceil</b> <start/end/step> (<i>analyze graphs for varying ceil reductions</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--reduce"></a><b>--reduce</b> (<i>use reduced matri [...]
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-These options cause analysis of a graph as it is subjected to reductions
-across a range of parameters. Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of
-these reductions. The analyses starts at the <i>end</i> argument, and
-progresses towards the <i>start</i> argument using decrements of size
-<i>step</i>. By default the reduction is always computed relative to the
-start matrix, i.e. the input matrix after <b>-tf</b> transformations have
-optionally been applied. Specifying <b>--reduce</b> causes this to change
-so that each new reduction is calculated relative to the reduction just
-computed.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For graphs with ties among edge weights it may be useful to use
-<b>-tf</b> <b>'#tug()'</b>. This will add small perturbations to the
-edge weights and have the effect of breaking ties.
-By default perturbations are computed using the cosine between
-the vectors of neighbours of the two nodes incident to an edge.
-This can be changed to a random perturbation with
-<b>-tf</b> <b>'#rug()'</b>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--test-cycle"></a><b>--test-cycle</b> (<i>test whether graph contains cycles</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-test-cycle"></a><b>-test-cycle</b> <num> (<i>test cycles, report cyclees</i>)</div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Test whether the input graph contains cycles. With the second option
-nodes that are part of a cycle are output, up to a maximum of <i><num></i>
-nodes. Use <i><num></i>=<b>-1</b> to output all such nodes.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--test-metric"></a><b>--test-metric</b> (<i>test whether graph distance is metric</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This tests all possible triangle relationships.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-div"></a><b>-div</b> <num> (<i>cluster size separating value</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-When analyzing graphs at different thresholds with one of the
-options above, <b>mcxquery</b> reports the percentage of nodes contained
-in clusters not exceeding a specified size, by default 3.
-This number can be changed using the <b>-div</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-t"></a><b>-t</b> <num> (<i>number of threads to use</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This has an effect only when using the <b>-vary-knn</b> option,
-and is only useful on multi-CPU machines.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--node-attr"></a><b>--node-attr</b> (<i>output node degree and weight attributes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output is in the form of a tab separated file.
-The option <b>-icl</b> can be used in conjuction.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>input clustering</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Output for each node the size of the cluster it is in.
-This option can be used in conjunction with <b>--node-attr</b>.
-</p>
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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-%%EOF
diff --git a/doc/mcxrand.1 b/doc/mcxrand.1
deleted file mode 100644
index 62a1edc..0000000
--- a/doc/mcxrand.1
+++ /dev/null
@@ -1,236 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxrand" 1 "16 May 2014" "mcxrand 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxrand \- random shuffling, removal, addition, and perturbation of edges of graphs
-.SH SYNOPSIS
-
-\fBmcxrand\fP [options]
-
-.di ZV
-.in 0
-.nf \fC
-mcxrand -gen K -add N -new-g-mean f # random graph on K nodes, N edges
-mcxrand -imx <name> -remove N -add N # remove then add edges
-mcxrand -imx <name> -shuffle N # shuffle N edge pairs
-mcxrand -imx <name> -noise-radius f # add noise to add weights
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-mcxrand -pa N/m # preferential attachment generation
-
-\fBmcxrand\fP
-\fB[-imx\fP <fname> (\fIinput matrix\fP)\fB]\fP
-\fB[-o\fP <fname> (\fIoutput matrix to <fname>\fP)\fB]\fP
-\fB[--write-binary\fP (\fIwrite output in binary format\fP)\fB]\fP
-\fB[-gen\fP <num> (\fIgenerate new graph\fP)\fB]\fP
-\fB[-pa\fP <N>/<m> (\fIpreferential attachment\fP)\fB]\fP
-\fB[-remove\fP <num> (\fIremove <num> edges\fP)\fB]\fP
-\fB[-add\fP <num> (\fIadd <num> edges not yet present\fP)\fB]\fP
-\fB[-shuffle\fP <num> (\fIshuffle edge pair <num> times\fP)\fB]\fP
-\fB[-icl\fP <fname> (\fIshuffle nodes preserving cluster sizes\fP)\fB]\fP
-\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
-\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
-.SH DESCRIPTION
-
-This utility is a recent addition to the mcl suite and the schemes
-explained below will likely be evolved, simplified, and extended
-with future releases\&.
-
-The \fB--shuffle\fP, \fB-gen\fP and \fB-pa\fP options can be deemend
-stable and robust\&. The options that determine edge weight perturbation and
-generation are likely to be subject to revision in the future\&.
-
-The input graph/matrix, if specified with the \fB-imx\fP option,
-has to be in mcl matrix/graph format\&.
-You can use label input instead by preprocessing the label input
-with \fBmcxload(1)\fP, i\&.e\&.
-
-.di ZV
-.in 0
-.nf \fC
- mcxload -abc <label-file> | mcxrand [options]
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-Refer to \fBmcxio(5)\fP for a description of these two input formats\&.
-By default \fBmcxrand\fP reads from STDIN\&. Change this with the \fB-imx\fP
-option\&.
-
-\fBmcxrand\fP can randomly remove and add edges to a graph, or add gaussian noise
-to the edge weights of a graph\&. It can also shuffle edge pairs while
-preserving the degree sequence of the graph\&.
-In \fIremoval mode\fP (\fB-remove\fP\ \&\fI<num>\fP) and in
-\fIaddition mode\fP (\fB-add\fP\ \&\fI<num>\fP)
-\fBmcxrand\fP enforces arc symmetry by only working with edges
-\fIw(i,j)\fP where \fIi < j\fP and symmetrifying the result and adding any
-loops that were present in the input graph just before the output stage\&.
-
-In \fIperturbation mode\fP (\fB-noise-radius\fP, with no other mode specified)
-the input can be any graph\&.
-
-\fIShuffle mode\fP (\fB-shuffle\fP\ \&\fI<num>\fP) requires an undirected graph
-but will only fail when it picks an arc for which the arc in the reverse
-direction is not present\&. This means it may or may not fail on directed
-input depending on the random choices\&. It does not check equality of the two
-arc weights and randomly picks one to represent the edge weight\&.
-
-Edge removal, edge creation, and edge perturbation are applied in this order
-if both are specified\&. Edge shuffling presently cannot be combined with one
-of the previous modes\&.
-
-A random graph can be generated with \fB-gen\fP\ \&\fIk\fP, which
-specifies the number of nodes the graph should have\&. It is equivalent
-with pasing (the file name of) an empty graph of the same dimensions as the argument
-to \fB-imx\fP\&.
-
-When adding (i\&.e\&. creating) edges, the default is to use the uniform
-distribution for new edge weights ranging in some interval\&.
-The default interval is [0,1] and can be modified using the
-\fB-edge-min\fP\ \&\fImin\fP and \fB-edge-max\fP\ \&\fImax\fP options\&.
-A Gaussian edge weight distribution can be obtained by specifying
-\fB-new-g-mean\fP\ \&\fInum\fP\&. The standard deviation is by default
-1\&.0 and can be altered with \fB-new-g-sdev\fP\ \&\fInum\fP\&.
-Currently the edge weigths are generated within the interval
-[\fImean-radius\fP, \fImean+radius\fP] where \fIradius\fP is specified
-with \fB-new-g-radius\fP\&. They are further selected to
-lie within the interval \fI[L,R]\fP if and only if
-\fB-new-g-min\fP\ \&\fIL\fP and \fB-new-g-max\fP\ \&\fIR\fP have
-been specified\&.
-
-For both uniform and Gaussian edge creation the edge weights
-can be skewed towards either side of the distribution with
-\fB-skew\fP\ \&\fIc\fP\&. Skewing is applied by mapping
-the edge weights to the interval [0,1], applying
-the function \fIx^c\fP, and remapping the resulting number\&.
-For values \fIc<1\fP this skews the edge weights towards
-the right bound and for values \fIc>1\fP this skews the edge
-weights towards the left bound\&.
-This is a rather crude approach that will likely be
-changed in the future\&.
-
-Edge weights can be perturbed by specifying \fB-noise-radius\fP\ \&\fIradius\fP\&.
-This sets the maximum perturbation allowed\&. Noise is generated with
-a standard deviation that is by default set to 0\&.5 and can be altered
-using \fB-noise-sdev\fP\ \&\fInum\fP\&.
-Values are generated in the interval \fI[-fac*sdev, fac*sdev]\fP
-where \fIfac\fP is set with \fB-noise-range\fP\ \&\fIfac\fP\&.
-This interval is mapped to the interval \fI[-radius, radius]\fP before
-the resulting value is added to the actual edge weight\&.
-This becomes the new value\&. If an interval \fI[L,R]\fP is explicitly
-specified using \fB-edge-min\fP\ \&\fIL\fP and \fB-edge-max\fP\ \&\fIR\fP
-then the new value will be accepted only if it lies within the interval,
-otherwise the edge will not be perturbed\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-The file name for input\&. STDIN is assumed if neither
-\fB-imx\fP nor \fB-gen\fP\ \&\fInum\fP is specified\&.
-.in -2m
-
-.ZI 2m "\fB-o\fP <fname> (\fIoutput matrix to <fname>\fP)"
-\&
-.br
-The file to write the transformed matrix to\&.
-.in -2m
-
-.ZI 2m "\fB--write-binary\fP (\fIwrite output in binary format\fP)"
-\&
-.br
-Write the output matrix in native binary format\&.
-.in -2m
-
-.ZI 2m "\fB-shuffle\fP <num> (\fIshuffle edge pair <num> times\fP)"
-\&
-.br
-Shuffle edge pair <num> times\&. An edge shuffle
-acts on two randomly chosen edges
-edges \fIw(a,b)\fP and \fIw(c,d)\fP where all the nodes must
-be different\&. If either none of the edges in \fIw(a,c)\fP, \fIw(b,d)\fP
-or none of the edges in \fIw(a,d)\fP, \fIw(b,c)\fP exists
-the original two edges are removed and is replaced
-by an edge pair for which both edges did not exist before\&.
-.in -2m
-
-.ZI 2m "\fB-icl\fP <fname> (\fIshuffle nodes preserving cluster sizes\fP)"
-\&
-.br
-Use this option to generate a random clustering with the exact same
-cluster size distribution as the input clustering\&.
-.in -2m
-
-.ZI 2m "\fB-pa\fP <N>/<m> (\fIpreferential attachment\fP)"
-\&
-.br
-This generates a random graph using preferential attachment\&.
-In this model new nodes are sequentially added to a graph\&.
-Each new node is connected with \fI<m>\fP of the existing
-nodes (including nodes previously added), where the likelihood
-of picking an existing node is proportional to the edge
-degree of that node\&. During construction multiple edges between
-two nodes are allowed (each with weight one), and these are collapsed by adding
-their weights before output\&.
-.in -2m
-
-.ZI 2m "\fB-remove\fP <num> (\fIremove <num> edges\fP)"
-\&
-.br
-Remove this many edges from the input graph\&.
-.in -2m
-
-.ZI 2m "\fB-add\fP <num> (\fIadd <num> edges not yet present\fP)"
-\&
-.br
-Create this many new edges\&.
-.in -2m
-
-.ZI 2m "\fB-gen\fP <num> (\fInode number\fP)"
-\&
-.br
-Use in conjunction with \fB-add\fP to generate
-a random graph on \fI<num>\fP nodes\&.
-.in -2m
-.SH SEE ALSO
-
-\fBmcxio(5)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxrand.html b/doc/mcxrand.html
deleted file mode 100644
index e32cdd8..0000000
--- a/doc/mcxrand.html
+++ /dev/null
@@ -1,304 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
-margin-left: 0%;
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-a.extern:link { color: #aa1111; }
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-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
-}
-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
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-.item_rightalign
-{ width: 2em;
-text-align: right;
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-{ position: absolute;
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-{ position: relative;
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-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
-margin-right: 8%;
-}
-</style>
-<title>The mcxrand manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxrand.ps"><b>mcxrand</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxrand — random shuffling, removal, addition, and perturbation of edges of graphs</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxrand</b> [options]
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<div class="verbatim">mcxrand -gen K -add N -new-g-mean f # random graph on K nodes, N edges
-mcxrand -imx <name> -remove N -add N # remove then add edges
-mcxrand -imx <name> -shuffle N # shuffle N edge pairs
-mcxrand -imx <name> -noise-radius f # add noise to add weights</div>
-mcxrand -pa N/m # preferential attachment generation</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxrand</b>
-<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output matrix to <fname></i>)<b>]</b></a>
-<a class="intern" href="#opt--write-binary"><b>[--write-binary</b> (<i>write output in binary format</i>)<b>]</b></a>
-<a class="intern" href="#opt-gen"><b>[-gen</b> <num> (<i>generate new graph</i>)<b>]</b></a>
-<a class="intern" href="#opt-pa"><b>[-pa</b> <N>/<m> (<i>preferential attachment</i>)<b>]</b></a>
-<a class="intern" href="#opt-remove"><b>[-remove</b> <num> (<i>remove <num> edges</i>)<b>]</b></a>
-<a class="intern" href="#opt-add"><b>[-add</b> <num> (<i>add <num> edges not yet present</i>)<b>]</b></a>
-<a class="intern" href="#opt-shuffle"><b>[-shuffle</b> <num> (<i>shuffle edge pair <num> times</i>)<b>]</b></a>
-<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>shuffle nodes preserving cluster sizes</i>)<b>]</b></a>
-<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
-<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-This utility is a recent addition to the mcl suite and the schemes
-explained below will likely be evolved, simplified, and extended
-with future releases.</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--shuffle</b>, <b>-gen</b> and <b>-pa</b> options can be deemend
-stable and robust. The options that determine edge weight perturbation and
-generation are likely to be subject to revision in the future.</p>
-<p style="margin-bottom:0" class="asd_par">
-The input graph/matrix, if specified with the <b>-imx</b> option,
-has to be in mcl matrix/graph format.
-You can use label input instead by preprocessing the label input
-with <a class="local sibling" href="mcxload.html">mcxload</a>, i.e.</p>
-<div class="verbatim"> mcxload -abc <label-file> | mcxrand [options]</div>
-<p style="margin-bottom:0" class="asd_par">
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of these two input formats.
-By default <b>mcxrand</b> reads from STDIN. Change this with the <a class="intern" href="#opt-imx"><b>-imx</b></a>
-option.</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxrand</b> can randomly remove and add edges to a graph, or add gaussian noise
-to the edge weights of a graph. It can also shuffle edge pairs while
-preserving the degree sequence of the graph.
-In <i>removal mode</i> (<a class="intern" href="#opt-remove"><b>-remove</b> <i><num></i></a>) and in
-<i>addition mode</i> (<a class="intern" href="#opt-add"><b>-add</b> <i><num></i></a>)
-<b>mcxrand</b> enforces arc symmetry by only working with edges
-<i>w(i,j)</i> where <i>i < j</i> and symmetrifying the result and adding any
-loops that were present in the input graph just before the output stage.</p>
-<p style="margin-bottom:0" class="asd_par">
-In <i>perturbation mode</i> (<a class="intern" href="#opt-noise-radius"><b>-noise-radius</b></a>, with no other mode specified)
-the input can be any graph.</p>
-<p style="margin-bottom:0" class="asd_par">
-<i>Shuffle mode</i> (<a class="intern" href="#opt-shuffle"><b>-shuffle</b> <i><num></i></a>) requires an undirected graph
-but will only fail when it picks an arc for which the arc in the reverse
-direction is not present. This means it may or may not fail on directed
-input depending on the random choices. It does not check equality of the two
-arc weights and randomly picks one to represent the edge weight.</p>
-<p style="margin-bottom:0" class="asd_par">
-Edge removal, edge creation, and edge perturbation are applied in this order
-if both are specified. Edge shuffling presently cannot be combined with one
-of the previous modes.</p>
-<p style="margin-bottom:0" class="asd_par">
-A random graph can be generated with <a class="intern" href="#opt-gen"><b>-gen</b> <i>k</i></a>, which
-specifies the number of nodes the graph should have. It is equivalent
-with pasing (the file name of) an empty graph of the same dimensions as the argument
-to <b>-imx</b>.</p>
-<p style="margin-bottom:0" class="asd_par">
-When adding (i.e. creating) edges, the default is to use the uniform
-distribution for new edge weights ranging in some interval.
-The default interval is [0,1] and can be modified using the
-<a class="intern" href="#opt-edge-min"><b>-edge-min</b> <i>min</i></a> and <a class="intern" href="#opt-edge-max"><b>-edge-max</b> <i>max</i></a> options.
-A Gaussian edge weight distribution can be obtained by specifying
-<a class="intern" href="#opt-new-g-mean"><b>-new-g-mean</b> <i>num</i></a>. The standard deviation is by default
-1.0 and can be altered with <a class="intern" href="#opt-new-g-sdev"><b>-new-g-sdev</b> <i>num</i></a>.
-Currently the edge weigths are generated within the interval
-[<i>mean-radius</i>, <i>mean+radius</i>] where <i>radius</i> is specified
-with <a class="intern" href="#opt-new-g-radius"><b>-new-g-radius</b></a>. They are further selected to
-lie within the interval <i>[L,R]</i> if and only if
-<a class="intern" href="#opt-new-g-min"><b>-new-g-min</b> <i>L</i></a> and <a class="intern" href="#opt-new-g-max"><b>-new-g-max</b> <i>R</i></a> have
-been specified.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For both uniform and Gaussian edge creation the edge weights
-can be skewed towards either side of the distribution with
-<a class="intern" href="#opt-skew"><b>-skew</b> <i>c</i></a>. Skewing is applied by mapping
-the edge weights to the interval [0,1], applying
-the function <i>x^c</i>, and remapping the resulting number.
-For values <i>c<1</i> this skews the edge weights towards
-the right bound and for values <i>c>1</i> this skews the edge
-weights towards the left bound.
-This is a rather crude approach that will likely be
-changed in the future.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Edge weights can be perturbed by specifying <a class="intern" href="#opt-noise-radius"><b>-noise-radius</b> <i>radius</i></a>.
-This sets the maximum perturbation allowed. Noise is generated with
-a standard deviation that is by default set to 0.5 and can be altered
-using <a class="intern" href="#opt-noise-sdev"><b>-noise-sdev</b> <i>num</i></a>.
-Values are generated in the interval <i>[-fac*sdev, fac*sdev]</i>
-where <i>fac</i> is set with <a class="intern" href="#opt-noise-range"><b>-noise-range</b> <i>fac</i></a>.
-This interval is mapped to the interval <i>[-radius, radius]</i> before
-the resulting value is added to the actual edge weight.
-This becomes the new value. If an interval <i>[L,R]</i> is explicitly
-specified using <a class="intern" href="#opt-edge-min"><b>-edge-min</b> <i>L</i></a> and <a class="intern" href="#opt-edge-max"><b>-edge-max</b> <i>R</i></a>
-then the new value will be accepted only if it lies within the interval,
-otherwise the edge will not be perturbed.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file name for input. STDIN is assumed if neither
-<b>-imx</b> nor <a class="intern" href="#opt-gen"><b>-gen</b> <i>num</i></a> is specified.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> <fname> (<i>output matrix to <fname></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The file to write the transformed matrix to.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--write-binary"></a><b>--write-binary</b> (<i>write output in binary format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Write the output matrix in native binary format.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-shuffle"></a><b>-shuffle</b> <num> (<i>shuffle edge pair <num> times</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Shuffle edge pair <num> times. An edge shuffle
-acts on two randomly chosen edges
-edges <i>w(a,b)</i> and <i>w(c,d)</i> where all the nodes must
-be different. If either none of the edges in <i>w(a,c)</i>, <i>w(b,d)</i>
-or none of the edges in <i>w(a,d)</i>, <i>w(b,c)</i> exists
-the original two edges are removed and is replaced
-by an edge pair for which both edges did not exist before.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>shuffle nodes preserving cluster sizes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this option to generate a random clustering with the exact same
-cluster size distribution as the input clustering.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-pa"></a><b>-pa</b> <N>/<m> (<i>preferential attachment</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This generates a random graph using preferential attachment.
-In this model new nodes are sequentially added to a graph.
-Each new node is connected with <i><m></i> of the existing
-nodes (including nodes previously added), where the likelihood
-of picking an existing node is proportional to the edge
-degree of that node. During construction multiple edges between
-two nodes are allowed (each with weight one), and these are collapsed by adding
-their weights before output.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-remove"></a><b>-remove</b> <num> (<i>remove <num> edges</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Remove this many edges from the input graph.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-add"></a><b>-add</b> <num> (<i>add <num> edges not yet present</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Create this many new edges.</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-gen"></a><b>-gen</b> <num> (<i>node number</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use in conjunction with <b>-add</b> to generate
-a random graph on <i><num></i> nodes.</p>
-</div>
-</div>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxio.html">mcxio</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.</p>
-</body>
-</html>
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diff --git a/doc/mcxsubs.1 b/doc/mcxsubs.1
deleted file mode 100644
index 3f9943b..0000000
--- a/doc/mcxsubs.1
+++ /dev/null
@@ -1,605 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxsubs" 1 "16 May 2014" "mcxsubs 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxsubs \- extract submatrices (subgraphs) of a matrix (graph)\&.
-
-\fBmcxsubs\fP can be used to
-inspect local cluster structure in a graph, for example by looking at the
-subgraph induced by a single cluster or a couple of clusterings, or the
-edge set where all tail nodes are from a set of domains and all head
-nodes are from the complement of this set, and many other variants and
-refinements\&.
-
-Additionally, mcxsubs enables
-
-.ZI 2m "\(bu"
-selecting matrix entries based on value\&.
-.in -2m
-.ZI 2m "\(bu"
-making the result characteristic (set all nonzero values to 1\&.0)\&.
-.in -2m
-.ZI 2m "\(bu"
-pruning empty columns and empty rows\&.
-.in -2m
-.ZI 2m "\(bu"
-transposing the result\&.
-.in -2m
-.ZI 2m "\(bu"
-remapping the indices of the result to consecutive indices\&.
-.in -2m
-.ZI 2m "\(bu"
-and other miscellaneous operations\&.
-.in -2m
-.SH SYNOPSIS
-
-\fBmcxsubs\fP \fB-imx\fP <fname> [options] <specs>+
-
-\fBmcxsubs\fP
-\fB-imx\fP <fname> (\fIinput matrix\fP)
-\fB[-dom\fP <fname> (\fIdomain matrix\fP)\fB]\fP
-\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
-\fB[--block\fP (\fIuse block matrix\fP)\fB]\fP
-\fB[--blockc\fP (\fIuse complement of block matrix\fP)\fB]\fP
-\fB[--skin-read\fP (\fIread domain structure without entries\fP)\fB]\fP
-\fB[--extend\fP (\fIread extended submatrices\fP)\fB]\fP
-\fB[-tab\fP (\fIread tab file\fP)\fB]\fP
-\fB[--from-disk\fP (\fIspace/speed optimizer\fP)\fB]\fP
-\fB[-out\fP <fname> (\fIspecial purpose output file name\fP)\fB]\fP
-\fB[-efac\fP <num> (\fIrandom edge selection\fP)\fB]\fP
-\fB[-dfac\fP <num> (\fIrandom domain selection\fP)\fB]\fP
-\fB[-rfac\fP <num> (\fIrandom column selection\fP)\fB]\fP
-\fB[-cfac\fP <num> (\fIrandom row selection\fP)\fB]\fP
-\fB[--rand-discard\fP (\fIremove random selections\fP)\fB]\fP
-\fB[--rand-merge\fP (\fImerge random selections\fP)\fB]\fP
-\fB[--rand-intersect\fP (\fIintersect random selections\fP)\fB]\fP
-\fB[--rand-exclusive\fP (\fIonly random selections\fP)\fB]\fP
-\fB[-tag-digits\fP k (\fIset precision\fP)\fB]\fP
-\fB[--tag\fP (\fItag nodes\fP)\fB]\fP
-<specs>+
-
-If you are a frequent \fBmcxsubs\fP user with very large graphs, consider
-converting the input matrix into binary format using
-\fBmcxconvert\fP and then using the mcxsubs
-\fB--from-disk\fP option\&. This should give you a 400-fold speed gain\&.
-.SH DESCRIPTION
-
-\fBmcxsubs\fP lets you extract submatrices/subgraphs corresponding with index
-sets and (possibly) sets of domains from a given domain matrix (e\&.g\&.
-a matrix representing a clustering)\&. Columns and
-rows of the target submatrix can be specified both independently and
-simultaneously, and can be specified as unions of simple index and domain
-ranges and complements of these\&.
-
-Because a submatrix or subgraph specification is composed of type,
-location, column, row, index, and set specifications,
-the word specification is
-abbreviated as spec\&. Multiple submatrices can be specified
-simultaneously\&. A submatrix is created for each submatrix spec\&. Everything
-encountered after the \fBmcxsubs\fP options are exhausted should be a spec\&.
-The syntax of specs is described in the \fBSUBMATRIX SPECIFICATIONS\fP section\&.
-By default, the domains of the submatrix will be set to the domains
-as described in the specification\&. This can be changed using the
-\fIuni\fP directives from the \fBfin\fP part\&.
-.SH OPTIONS
-
-.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
-\&
-.br
-Submatrices will all be selected from the matrix in file \fC<fname>\fP\&.
-This option is obligatory, and throughout this manual its argument
-is called the \fIsource matrix\fP\&.
-.in -2m
-
-.ZI 2m "\fB-dom\fP <fname> (\fIdomain matrix\fP)"
-\&
-.br
-Submatrices are specified in terms of sets (or domains) of
-indices\&. These sets are specified by (the label of) the vectors
-from the matrix given by this options\&.
-.in -2m
-
-.ZI 2m "\fB--block\fP (\fIuse block matrix\fP)"
-\&
-.br
-This replaces the input matrix by the block diagonal matrix
-induced by the domain matrix specified by the \fB-dom\fP option\&.
-It works by including a block for each domain in the domain matrix,
-and will work if there are overlapping domains\&. That is, it
-will not include overlapping parts more than once\&.
-The output file name can either be specified in the submatrix
-specification language using the \fBout\fP(\fIfname\fP) directive,
-or with the \fB-out\fP option\&.
-.in -2m
-
-.ZI 2m "\fB--blockc\fP (\fIuse complement of block matrix\fP)"
-\&
-.br
-This replaces the input matrix by the complement of the block diagonal
-matrix described above, and selection of the output name
-is exactly the same\&.
-.in -2m
-
-.ZI 2m "\fB--skin-read\fP (\fIread domain structure without entries\fP)"
-\&
-.br
-This reads a skeleton matrix by only considering its domain structure
-and not reading any entries, pertaining to the matrix
-specified by the \fB-imx\fP option\&.
-Transform the input matrix values according
-to the syntax described in \fBmcxio(5)\fP\&.
-.in -2m
-
-.ZI 2m "\fB-tab\fP (\fIread tab file\fP)"
-\&
-.br
-Read a tab file\&. Its domain can be used by the \fCt\fP and \fCT\fP
-indicators\&.
-.in -2m
-
-.ZI 2m "\fB--extend\fP (\fIread extended submatrices\fP)"
-\&
-.br
-This causes the selection of submatrices where either a row index
-is in the selected row domain or a columns index is in the selected
-column domain or both\&. Equivalently it only excludes matrix entries
-for which neither the column nor row index is in the selected domains\&.
-The resulting matrix has both domains equal to the source matrix\&.
-.in -2m
-
-.ZI 2m "\fB-out\fP <fname> (\fIspecial purpose output file name\fP)"
-\&
-.br
-This specifies an output name that can be used for special purposes\&.
-Normally, output file names are specified in the submatrix specification
-using the \fBout\fP(\fIfname\fP) directive\&.
-.in -2m
-
-.ZI 2m "\fB-efac\fP <num> (\fIrandom edge selection\fP)"
-\&
-.br
-\fInum\fP should be inbetween zero and one\&. It denotes the probability
-with which each edge is selected\&.
-.in -2m
-
-.ZI 2m "\fB-dfac\fP <num> (\fIrandom domain selection\fP)"
-\&
-.br
-\fInum\fP should be inbetween zero and one\&. It denotes the probability
-with which entries in the domains will make it into the randomized
-selection used for subsequent processing\&. By default the randomized
-selection is intersected with whatever the other selection criteria (if any)
-yield, i\&.e\&. the behaviour under the \fB--rand-intersect\fP option\&.
-
-If the column and row domain are identical, they are submitted to
-the same selection process and will end up identical\&. If you don\&'t want
-this, use \fB-rfac\fP and \fB-cfac\fP separately\&.
-
-If you just want a randomized selection, doing
-
-.di ZV
-.in 0
-.nf \fC
-mcxsubs -imx foo -dfac 0\&.5 \&'out(foo\&.rnd)\&'
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-will not yield the expected result\&. Randomized selections only work
-if a domain has explicitly been specified\&. The minimal way to achieve
-this is the following:
-
-.di ZV
-.in 0
-.nf \fC
-mcxsubs -imx foo -dfac 0\&.5 \&'dom(cr), out(foo\&.rnd)\&'
-.fi \fR
-.in
-.di
-.ne \n(dnu
-.nf \fC
-.ZV
-.fi \fR
-
-.in -2m
-
-.ZI 2m "\fB-rfac\fP <num> (\fIrandom column selection\fP)"
-\&
-.br
-As \fB-dfac\fP, limited to the column domain\&.
-.in -2m
-
-.ZI 2m "\fB-cfac\fP <num> (\fIrandom row selection\fP)"
-\&
-.br
-As \fB-dfac\fP, limited to the row domain\&.
-.in -2m
-
-.ZI 2m "\fB--rand-merge\fP (\fImerge random selections\fP)"
-\&
-.br
-The random selection(s) of domains identify parts of the
-matrix that will be merged with the result of the main
-selection process (default)\&.
-.in -2m
-
-.ZI 2m "\fB--rand-discard\fP (\fIremove random selections\fP)"
-\&
-.br
-The random selection(s) of domains identify parts of the
-matrix that will be removed from the result of the main
-selection process\&.
-.in -2m
-
-.ZI 2m "\fB--rand-intersect\fP (\fIintersect random selections\fP)"
-\&
-.br
-The random selection(s) of domains identify parts of the
-matrix that will be intersected with the result of the main
-selection process\&. This is the default\&.
-.in -2m
-
-.ZI 2m "\fB--rand-exclusive\fP (\fIonly random selections\fP)"
-\&
-.br
-The random selection(s) of domains identify parts of the
-matrix from which the result of the main
-selection process will be removed\&.
-.in -2m
-
-.ZI 2m "\fB-tag-digits\fP k (\fIset precision\fP)"
-\&
-.br
-Sets the precision for tagged output\&.
-Setting it to \fB-tag-digits\fP\ \&\fB-1\fP
-disables the output of values altogether \- only the node indices
-and the cluster indices are written\&.
-.in -2m
-
-.ZI 2m "\fB--tag\fP (\fItag nodes\fP)"
-\&
-.br
-Each node in the column (tail node) listing of the matrix (graph)
-spec is tagged with the domain it is in\&. This requires
-the use of the \fB-dom\fP option\&.
-This output mode, called \fItagged matrix\fP, is currently not
-recognized by any of the \fBmcl\fP/\fBmcx\fP input routines\&. It is present
-to facilitate easier visual inspection of clustering results\&.
-.in -2m
-
-.ZI 2m "\fB--from-disk\fP (\fIspace/speed optimizer\fP)"
-\&
-.br
-Use this if the input graph is in binary format, or if the
-input graph is very large and the subgraph(s) to extract
-are small in comparison, or if the available memory
-does not comfortably exceed the size of the graph\&.
-
-The effect of this option is that the subgraph will be read
-directly from disk, without reading in the entire graph
-in advance\&. This will be done repeatedly for all subgraphs that are
-specified\&.
-
-This option reduces memory consumption to the size of the subgraph(s)
-to be extracted\&.
-
-For graphs in interchange format, the speed gain is not
-dramatic\&. If more than one subgraph is specified, there will most
-likely be a loss in speed\&.
-
-With input graphs in binary format, \fBmcxsubs\fP will
-be *very* much faster, to the extent of 400-fold speed gains\&.
-It does not matter whether more than one subgraph is specified\&.
-.in -2m
-.SH SUBMATRIX SPECIFICATIONS
-
-A submatrix or subgraph spec may contain a number of spec parts\&. Each part
-is specified in a function-style notation\&. Different parts are separated by
-commas\&. Parts may occur multiple times, but for most parts only the last one
-specified will be effective\&. The spec parts are the following: \fBdom\fP,
-\fBext\fP, \fBval\fP, \fBsize\fP, \fBfin\fP, and \fBout\fP\&. These are described
-below in the sections DOMAINS, EXTENSION, VALUES, SIZE, FINALIZE and OUTPUT\&.
-
-\fBDOMAINS\fP
-.br
-The domain part is specified as
-
-\fBdom\fP(\fIX\fP <, \fIY\fP(\fIispec\fP) >+)
-
-Here \fIX\fP is the row/column indicator\&. Rows are indicated with
-either \fCr\fP or \fCR\fP, columns are indicated with either
-\fCc\fP or \fCC\fP\&. \fIX\fP may contain one or two indicators, with
-a single indicator per column domain and row domain allowed\&.
-Uppercase indicators indicate that the complement is being specified
-relative to the corresponding domain in the target matrix\&.
-
-\fIY\fP is the type indicator, it is exactly one of
-\fCi\fP, \fCI\fP, \fCd\fP, \fCD\fP, \fCc\fP, \fCr\fP, \fCt\fP, or \fCT\fP\&.
-The \fCi/I\fP indicators specify
-that \fIispec\fP contains a simple index specifation\&.
-The \fCd/D\fP specify that \fIispec\fP contains domain indices\&.
-\fIispec\fP must contain a comma-separated list of integers or
-integer ranges (e\&.g\&. 2, 5, 4-8)\&.
-\fCc\fP and \fCr\fP are restricted indicators that refer
-to the domains in the \fIdomain matrix\fP\&.
-\fCt\fP and \fCT\fP are restricted indicators that refer
-to the domain encoded in the tab file as specified by the
-\fB-tab\fP option\&. Their usage is described further below\&.
-
-For domain specifications (\fCd/D\fP) the columns indexed by
-these integers in the matrix specified in the \fB-dom\fP
-option will be fetched and merged\&. If \fB-dom\fP was not used
-the target matrix itself (as specified by the \fB-imx\fP option) will be
-used\&. For simple specifications
-(\fCi/I\fP) the result is simply the list of integers itself\&. Uppercase
-indicators indicate that the complement is being specified\&.
-
-Examples:
-
-.ZI 2m "\fCdom(cr, i(0-6,10,11-14))\fP"
-\&
-.br
-Principal submatrix on indices 0-6, 10, and 11-14 \- all column and row
-indices are from this set\&. Equivalently, this encodes the subgraph on
-nodes 0-6, 10, 11-14\&. The \&'c\&' stands for column, the \&'r\&' for row, and the
-\&'i\&' for index\&. It is also possible to specify a \&'d\&' part
-(standing for domain), this is shown further below\&.
-.in -2m
-
-.ZI 2m "\fCdom(c, i(0-6,10,11-14)), dom(r, i(1-6,10,11-14))\fP"
-\&
-.br
-Equivalent (but less clear) spec of the above\&.
-.in -2m
-
-.ZI 2m "\fCdom(cR, i(0-6,10,11-14))\fP"
-\&
-.br
-Matrix with column indices in 0-6, 10, 11-14, and row indices
-in the complement of this set\&. Corresponds with all edges going
-\fIout\fP from the set 0-6, 10, 11-14\&. Complements are triggered
-by the use of a capital; see the next examples\&.
-.in -2m
-
-.ZI 2m "\fCdom(c, i(0-6,10,11-14)), dom(R, i(1-6,10,11-14))\fP"
-\&
-'in -2m
-.ZI 2m "\fCdom(c, i(0-6,10,11-14)), dom(r, I(1-6,10,11-14))\fP"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Both these examples are equivalent to the previous one\&.
-In the last example, the capital \&'I\&' indicates that the complement
-should be taken\&. In this example, \&'r\&' combined with \&'I\&' has the
-same effect as \&'R\&' combined with \&'i\&'\&.
-.in -2m
-
-.ZI 2m "\fCdom(c, d(3,5-9)), dom(r, d(8-14), i(10-30))\fP"
-\&
-.br
-Column indices are taken from the domains 3, 5-9 (from the
-domain matrix specified by \fB-dom\fP), row indices are taken
-from domains 8-14 plus the indices 10-30\&.
-.in -2m
-
-.ZI 2m "\fCdom(cR, d(0-2))\fP"
-\&
-.br
-Column indices are all indices from domains 0-2, row indices
-are all other indices\&. This gives all edges going \fIout\fP
-from domains 0-2\&.
-
-The use of \&'D\&' is analogous to that of \&'C\&', \&'R\&', and \&'I\&'\&.
-Thus, \fCD(0-3,8,21-30)\fP specifies all indices which are in the
-complement of the set formed by taking the union of
-domains 0-3,8,21-30\&.
-.in -2m
-
-The \fCc\fP and \fCr\fP indicators must be followed by a
-pair of matching parentheses\&. They specify to take respectively
-the column domain and the row domain of the domain matrix (cf\&. \fB-dom\fP)\&.
-
-The \fCt\fP and \fCT\fP indicators must be followed by a
-pair of matching parentheses\&. They specify to take the domain
-found in the tab file or its complement\&.
-
-As seen above, indices (either representing themselves or domains) are
-entered as comma-separated lists of single indices, ranges of indices
-(which may overlap), or staircases of indices (lists of indices with
-a fixed increment inbetween successive indices)\&.
-The union of the corresponding elements is taken and
-passed along\&. Before anything else, the result set is replaced by its
-complement if \&'I\&' is specified (for simple indices) or \&'D\&' is specified
-(for domains)\&. If there is both an index and a set spec string, the
-union of the results of both is taken and passed along\&. If the latter
-result is passed to either \&'C\&' or \&'R\&', it is replaced by its complement\&.
-
-A range is specified e\&.g\&. as \fC10-14\fP and it is inclusive, denoting
-in this case the indices \fC{10,11,12,13,14}\fP\&.
-
-\fBEXTENSION\fP
-.br
-The extension part is specified as
-
-\fBext\fP( < \fBdisc\fP(\fIk\fP) | \fBcdisc\fP(\fIk\fP) | \fBrdisc\fP(\fIk\fP) >)
-
-This option requires the input matrix to be held in memory\&. This implies it
-will not work with the \fB--from-disk\fP option\&.
-
-This \fIassumes that the input matrix encodes a graph\fP, so the column
-and row domains must be equal\&.
-It will take the currently selected domain (column domain for
-\fBdisc\fP and \fBcdisc\fP, row domain for \fBrdisc\fP), and add
-all nodes to it that are reachable in \fIk\fP steps\&.
-The \fBdisc\fP variant replaces both column and row domains by
-the extended domain, the other variants just change a single domain\&.
-
-Setting \fIk\fP to \fC-1\fP results in adding \fIall\fP nodes that
-can be reached from the start domain\&.
-
-\fBVALUES\fP
-.br
-The value part is specified as
-
-\fBval\fP(<tf-spec>)
-
-It transforms or removes values according to \fI<tf-spec>\fP\&.
-Refer to \fBmcxio(5)\fP for a description of the transformation
-specification syntax and the available transformation primitives\&.
-
-\fBSIZE\fP
-.br
-The size part is specified as
-
-\fBsize\fP( < \fBlt\fP(\fIx\fP) | \fBceil\fP(\fIx\fP) | \fBgq\fP(\fIx\fP) | \fBrmgq\fP(\fIx\fP) > + )
-
-Where \fIx\fP is a nonnegative integer, and multiple specifications
-are separated by commas\&.
-The strings \&'lt\&', \&'lq\&', \&'gq\&', \&'gt\&', respectively denote
-\fIless than\fP,
-\fIless than or equal to\fP,
-\fIgreater than or equal to\fP,
-and
-\fIgreater than\fP\&.
-
-This prunes or removes column vectors based on their size\&. If \fBlt\fP
-is used, column vectors are removed if the number of entries exceeds
-the specified bound\&. If \fBgq\fP is used, vectors are discarded
-if the number of entries is smaller than the specified bound\&. If a column
-vector has an excess of entries over the bound specified by \fBceil\fP, the
-smallest entries are removed\&. Ties are not arbitrarily broken, implying that
-the resulting vector may still have more entries than the specified bound\&.
-
-\fBFINALIZE\fP
-.br
-The finalize part is specified as
-\fBfin\fP( < \fIkey\fP > )
-where \fIkey\fP is a string and multiple keys are separated by commas\&. The
-corresponding actions are generally applied to the matrix that was extracted
-according to the domain and value specifications\&. Exceptions are indicated
-below\&. Currently, there is a fixed order in which actions are considered,
-corresponding with the order in which they are listed below\&.
-
-.ZI 2m "skel"
-\&
-.br
-This creates an empty submatrix on the specified domains, and does
-\fInot\fP fill it with the corresponding entries from the
-source matrix\&.
-Options from the \fBfin\fP part that affect the column and
-row domains of a matrix will still be in effect\&.
-.in -2m
-
-.ZI 2m "uni"
-\&
-'in -2m
-.ZI 2m "unir"
-\&
-'in -2m
-.ZI 2m "unic"
-\&
-'in -2m
-'in +2m
-\&
-.br
-After the submatrix is selected from the source matrix, its domains
-are changed to mirror one or both of the domains of the source matrix\&.
-.in -2m
-
-.ZI 2m "tp"
-\&
-.br
-The resulting submatrix is replaced by its transpose\&.
-.in -2m
-
-.ZI 2m "cc"
-\&
-.br
-The resulting submatrix is made characteristic\&.
-.in -2m
-
-.ZI 2m "scrubc"
-\&
-'in -2m
-.ZI 2m "scrubr"
-\&
-'in -2m
-.ZI 2m "scrubg"
-\&
-'in -2m
-.ZI 2m "scrub"
-\&
-'in -2m
-'in +2m
-\&
-.br
-Domains are shrunk if there are no corresponding entries in the matrix\&.
-This is done for both domains if \fCscrub\fP is specified, for the
-column domain if \fCscrubc\fP is specified, and for the row domain
-if \fCscrubr\fP is specified\&. Thus, with \fCscrubc\fP columns are removed
-from the domain and the matrix if they are empty\&.
-With \fCscrubg\fP the union of the resulting domains is taken\&.
-.in -2m
-
-.ZI 2m "mapc"
-\&
-'in -2m
-.ZI 2m "mapr"
-\&
-'in -2m
-.ZI 2m "map"
-\&
-'in -2m
-'in +2m
-\&
-.br
-The appropriate domains are mapped onto consecutive indices starting at zero\&.
-.in -2m
-
-\fBOUTPUT\fP
-.br
-The output part is specified as
-\fBout\fP( \fIfname\fP <, \fIkey\fP >* )
-that is, the \fIfname\fP option is obligatory if the \fBout\fP part is specified\&.
-Currently, key can be a single directive, namely \fBwb\fP specifying that
-the resulting matrix should be output in binary format\&.
-.SH AUTHOR
-
-Stijn van Dongen\&.
-.SH SEE ALSO
-
-\fBmcx(1)\fP,
-and \fBmclfamily(7)\fP for an overview of all the documentation
-and the utilities in the mcl family\&.
diff --git a/doc/mcxsubs.html b/doc/mcxsubs.html
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-<title>The mcxsubs manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxsubs.ps"><b>mcxsubs</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#spec">SUBMATRIX SPECIFICATIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#seealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxsubs — extract submatrices (subgraphs) of a matrix (graph).</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxsubs</b> can be used to
-inspect local cluster structure in a graph, for example by looking at the
-subgraph induced by a single cluster or a couple of clusterings, or the
-edge set where all tail nodes are from a set of domains and all head
-nodes are from the complement of this set, and many other variants and
-refinements.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Additionally, mcxsubs enables
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-selecting matrix entries based on value.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-making the result characteristic (set all nonzero values to 1.0).
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-pruning empty columns and empty rows.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-transposing the result.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-remapping the indices of the result to consecutive indices.
-</p>
-</div>
-<div class=" item_compact"><div class=" item_leftalign " ><span class="itembullet">•</span></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-and other miscellaneous operations.
-</p>
-</div>
-</div>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxsubs</b> <b>-imx</b> <fname> [options] <specs>+
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxsubs</b>
-<a class="intern" href="#opt-imx"><b>-imx</b> <fname> (<i>input matrix</i>)</a>
-<a class="intern" href="#opt-dom"><b>[-dom</b> <fname> (<i>domain matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--block"><b>[--block</b> (<i>use block matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--blockc"><b>[--blockc</b> (<i>use complement of block matrix</i>)<b>]</b></a>
-<a class="intern" href="#opt--skin-read"><b>[--skin-read</b> (<i>read domain structure without entries</i>)<b>]</b></a>
-<a class="intern" href="#opt--extend"><b>[--extend</b> (<i>read extended submatrices</i>)<b>]</b></a>
-<a class="intern" href="#opt-tab"><b>[-tab</b> (<i>read tab file</i>)<b>]</b></a>
-<a class="intern" href="#opt--from-disk"><b>[--from-disk</b> (<i>space/speed optimizer</i>)<b>]</b></a>
-<a class="intern" href="#opt-out"><b>[-out</b> <fname> (<i>special purpose output file name</i>)<b>]</b></a>
-<a class="intern" href="#opt-efac"><b>[-efac</b> <num> (<i>random edge selection</i>)<b>]</b></a>
-<a class="intern" href="#opt-dfac"><b>[-dfac</b> <num> (<i>random domain selection</i>)<b>]</b></a>
-<a class="intern" href="#opt-rfac"><b>[-rfac</b> <num> (<i>random column selection</i>)<b>]</b></a>
-<a class="intern" href="#opt-cfac"><b>[-cfac</b> <num> (<i>random row selection</i>)<b>]</b></a>
-<a class="intern" href="#opt--rand-discard"><b>[--rand-discard</b> (<i>remove random selections</i>)<b>]</b></a>
-<a class="intern" href="#opt--rand-merge"><b>[--rand-merge</b> (<i>merge random selections</i>)<b>]</b></a>
-<a class="intern" href="#opt--rand-intersect"><b>[--rand-intersect</b> (<i>intersect random selections</i>)<b>]</b></a>
-<a class="intern" href="#opt--rand-exclusive"><b>[--rand-exclusive</b> (<i>only random selections</i>)<b>]</b></a>
-<a class="intern" href="#opt-tag-digits"><b>[-tag-digits</b> k (<i>set precision</i>)<b>]</b></a>
-<a class="intern" href="#opt--tag"><b>[--tag</b> (<i>tag nodes</i>)<b>]</b></a>
-<specs>+
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If you are a frequent <b>mcxsubs</b> user with very large graphs, consider
-converting the input matrix into binary format using
-<b>mcxconvert</b> and then using the mcxsubs
-<b>--from-disk</b> option. This should give you a 400-fold speed gain.
-</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxsubs</b> lets you extract submatrices/subgraphs corresponding with index
-sets and (possibly) sets of domains from a given domain matrix (e.g.
-a matrix representing a clustering). Columns and
-rows of the target submatrix can be specified both independently and
-simultaneously, and can be specified as unions of simple index and domain
-ranges and complements of these.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Because a submatrix or subgraph specification is composed of type,
-location, column, row, index, and set specifications,
-the word specification is
-abbreviated as spec. Multiple submatrices can be specified
-simultaneously. A submatrix is created for each submatrix spec. Everything
-encountered after the <b>mcxsubs</b> options are exhausted should be a spec.
-The syntax of specs is described in the <a class="intern" href="#spec">SUBMATRIX SPECIFICATIONS</a> section.
-By default, the domains of the submatrix will be set to the domains
-as described in the specification. This can be changed using the
-<i>uni</i> directives from the <b>fin</b> part.
-</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Submatrices will all be selected from the matrix in file <tt><fname></tt>.
-This option is obligatory, and throughout this manual its argument
-is called the <i>source matrix</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dom"></a><b>-dom</b> <fname> (<i>domain matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Submatrices are specified in terms of sets (or domains) of
-indices. These sets are specified by (the label of) the vectors
-from the matrix given by this options.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--block"></a><b>--block</b> (<i>use block matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This replaces the input matrix by the block diagonal matrix
-induced by the domain matrix specified by the <b>-dom</b> option.
-It works by including a block for each domain in the domain matrix,
-and will work if there are overlapping domains. That is, it
-will not include overlapping parts more than once.
-The output file name can either be specified in the submatrix
-specification language using the <b>out</b>(<i>fname</i>) directive,
-or with the <b>-out</b> option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--blockc"></a><b>--blockc</b> (<i>use complement of block matrix</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This replaces the input matrix by the complement of the block diagonal
-matrix described above, and selection of the output name
-is exactly the same.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--skin-read"></a><b>--skin-read</b> (<i>read domain structure without entries</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This reads a skeleton matrix by only considering its domain structure
-and not reading any entries, pertaining to the matrix
-specified by the <b>-imx</b> option.
-</p>
-Transform the input matrix values according
-to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> (<i>read tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Read a tab file. Its domain can be used by the <tt>t</tt> and <tt>T</tt>
-indicators.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--extend"></a><b>--extend</b> (<i>read extended submatrices</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This causes the selection of submatrices where either a row index
-is in the selected row domain or a columns index is in the selected
-column domain or both. Equivalently it only excludes matrix entries
-for which neither the column nor row index is in the selected domains.
-The resulting matrix has both domains equal to the source matrix.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-out"></a><b>-out</b> <fname> (<i>special purpose output file name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-This specifies an output name that can be used for special purposes.
-Normally, output file names are specified in the submatrix specification
-using the <b>out</b>(<i>fname</i>) directive.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-efac"></a><b>-efac</b> <num> (<i>random edge selection</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<i>num</i> should be inbetween zero and one. It denotes the probability
-with which each edge is selected.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dfac"></a><b>-dfac</b> <num> (<i>random domain selection</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-<i>num</i> should be inbetween zero and one. It denotes the probability
-with which entries in the domains will make it into the randomized
-selection used for subsequent processing. By default the randomized
-selection is intersected with whatever the other selection criteria (if any)
-yield, i.e. the behaviour under the <b>--rand-intersect</b> option.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If the column and row domain are identical, they are submitted to
-the same selection process and will end up identical. If you don't want
-this, use <b>-rfac</b> and <b>-cfac</b> separately.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-If you just want a randomized selection, doing</p>
-<div class="verbatim">mcxsubs -imx foo -dfac 0.5 'out(foo.rnd)'</div>
-<p style="margin-top:0em; margin-bottom:0em">
-will not yield the expected result. Randomized selections only work
-if a domain has explicitly been specified. The minimal way to achieve
-this is the following:</p>
-<div class="verbatim">mcxsubs -imx foo -dfac 0.5 'dom(cr), out(foo.rnd)'</div>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-rfac"></a><b>-rfac</b> <num> (<i>random column selection</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-As <b>-dfac</b>, limited to the column domain.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cfac"></a><b>-cfac</b> <num> (<i>random row selection</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-As <b>-dfac</b>, limited to the row domain.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rand-merge"></a><b>--rand-merge</b> (<i>merge random selections</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The random selection(s) of domains identify parts of the
-matrix that will be merged with the result of the main
-selection process (default).
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rand-discard"></a><b>--rand-discard</b> (<i>remove random selections</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The random selection(s) of domains identify parts of the
-matrix that will be removed from the result of the main
-selection process.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rand-intersect"></a><b>--rand-intersect</b> (<i>intersect random selections</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The random selection(s) of domains identify parts of the
-matrix that will be intersected with the result of the main
-selection process. This is the default.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rand-exclusive"></a><b>--rand-exclusive</b> (<i>only random selections</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-The random selection(s) of domains identify parts of the
-matrix from which the result of the main
-selection process will be removed.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tag-digits"></a><b>-tag-digits</b> k (<i>set precision</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Sets the precision for tagged output.
-Setting it to <b>-tag-digits</b> <b>-1</b>
-disables the output of values altogether — only the node indices
-and the cluster indices are written.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--tag"></a><b>--tag</b> (<i>tag nodes</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Each node in the column (tail node) listing of the matrix (graph)
-spec is tagged with the domain it is in. This requires
-the use of the <b>-dom</b> option.
-This output mode, called <i>tagged matrix</i>, is currently not
-recognized by any of the <b>mcl</b>/<b>mcx</b> input routines. It is present
-to facilitate easier visual inspection of clustering results.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--from-disk"></a><b>--from-disk</b> (<i>space/speed optimizer</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this if the input graph is in binary format, or if the
-input graph is very large and the subgraph(s) to extract
-are small in comparison, or if the available memory
-does not comfortably exceed the size of the graph.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The effect of this option is that the subgraph will be read
-directly from disk, without reading in the entire graph
-in advance. This will be done repeatedly for all subgraphs that are
-specified.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This option reduces memory consumption to the size of the subgraph(s)
-to be extracted.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For graphs in interchange format, the speed gain is not
-dramatic. If more than one subgraph is specified, there will most
-likely be a loss in speed.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-With input graphs in binary format, <b>mcxsubs</b> will
-be *very* much faster, to the extent of 400-fold speed gains.
-It does not matter whether more than one subgraph is specified.
-</p>
-</div>
-</div>
-
-<a name="spec"></a>
-<h2>SUBMATRIX SPECIFICATIONS</h2>
-<p style="margin-bottom:0" class="asd_par">
-A submatrix or subgraph spec may contain a number of spec parts. Each part
-is specified in a function-style notation. Different parts are separated by
-commas. Parts may occur multiple times, but for most parts only the last one
-specified will be effective. The spec parts are the following: <b>dom</b>,
-<b>ext</b>, <b>val</b>, <b>size</b>, <b>fin</b>, and <b>out</b>. These are described
-below in the sections DOMAINS, EXTENSION, VALUES, SIZE, FINALIZE and OUTPUT.
-</p>
-<p style="margin-bottom:0"><b>DOMAINS</b><br>
-The domain part is specified as
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>dom</b>(<i>X</i> <, <i>Y</i>(<i>ispec</i>) >+)
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Here <i>X</i> is the row/column indicator. Rows are indicated with
-either <tt>r</tt> or <tt>R</tt>, columns are indicated with either
-<tt>c</tt> or <tt>C</tt>. <i>X</i> may contain one or two indicators, with
-a single indicator per column domain and row domain allowed.
-Uppercase indicators indicate that the complement is being specified
-relative to the corresponding domain in the target matrix.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<i>Y</i> is the type indicator, it is exactly one of
-<tt>i</tt>, <tt>I</tt>, <tt>d</tt>, <tt>D</tt>, <tt>c</tt>, <tt>r</tt>, <tt>t</tt>, or <tt>T</tt>.
-The <tt>i/I</tt> indicators specify
-that <i>ispec</i> contains a simple index specifation.
-The <tt>d/D</tt> specify that <i>ispec</i> contains domain indices.
-<i>ispec</i> must contain a comma-separated list of integers or
-integer ranges (e.g. 2, 5, 4-8).
-<tt>c</tt> and <tt>r</tt> are restricted indicators that refer
-to the domains in the <i>domain matrix</i>.
-<tt>t</tt> and <tt>T</tt> are restricted indicators that refer
-to the domain encoded in the tab file as specified by the
-<b>-tab</b> option. Their usage is described further below.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-For domain specifications (<tt>d/D</tt>) the columns indexed by
-these integers in the matrix specified in the <b>-dom</b>
-option will be fetched and merged. If <b>-dom</b> was not used
-the target matrix itself (as specified by the <b>-imx</b> option) will be
-used. For simple specifications
-(<tt>i/I</tt>) the result is simply the list of integers itself. Uppercase
-indicators indicate that the complement is being specified.
-</p>
-<p style="margin-bottom:0" class="asd_par">Examples:</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>dom(cr, i(0-6,10,11-14))</tt></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Principal submatrix on indices 0-6, 10, and 11-14 — all column and row
-indices are from this set. Equivalently, this encodes the subgraph on
-nodes 0-6, 10, 11-14. The 'c' stands for column, the 'r' for row, and the
-'i' for index. It is also possible to specify a 'd' part
-(standing for domain), this is shown further below.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>dom(c, i(0-6,10,11-14)), dom(r, i(1-6,10,11-14))</tt></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Equivalent (but less clear) spec of the above.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>dom(cR, i(0-6,10,11-14))</tt></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Matrix with column indices in 0-6, 10, 11-14, and row indices
-in the complement of this set. Corresponds with all edges going
-<i>out</i> from the set 0-6, 10, 11-14. Complements are triggered
-by the use of a capital; see the next examples.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><tt>dom(c, i(0-6,10,11-14)), dom(R, i(1-6,10,11-14))</tt></div><div class=" item_cascade item_leftalign nowrap" ><tt>dom(c, i(0-6,10,11-14)), dom(r, I(1-6,10,11-14))</tt></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Both these examples are equivalent to the previous one.
-In the last example, the capital 'I' indicates that the complement
-should be taken. In this example, 'r' combined with 'I' has the
-same effect as 'R' combined with 'i'.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>dom(c, d(3,5-9)), dom(r, d(8-14), i(10-30))</tt></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Column indices are taken from the domains 3, 5-9 (from the
-domain matrix specified by <b>-dom</b>), row indices are taken
-from domains 8-14 plus the indices 10-30.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><tt>dom(cR, d(0-2))</tt></div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Column indices are all indices from domains 0-2, row indices
-are all other indices. This gives all edges going <i>out</i>
-from domains 0-2.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The use of 'D' is analogous to that of 'C', 'R', and 'I'.
-Thus, <tt>D(0-3,8,21-30)</tt> specifies all indices which are in the
-complement of the set formed by taking the union of
-domains 0-3,8,21-30.
-</p>
-</div>
-</div>
-<p style="margin-bottom:0" class="asd_par">
-The <tt>c</tt> and <tt>r</tt> indicators must be followed by a
-pair of matching parentheses. They specify to take respectively
-the column domain and the row domain of the domain matrix (cf. <a class="intern" href="#opt-dom"><b>-dom</b></a>).
-</p>
-<p style="margin-bottom:0" class="asd_par">
-The <tt>t</tt> and <tt>T</tt> indicators must be followed by a
-pair of matching parentheses. They specify to take the domain
-found in the tab file or its complement.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-As seen above, indices (either representing themselves or domains) are
-entered as comma-separated lists of single indices, ranges of indices
-(which may overlap), or staircases of indices (lists of indices with
-a fixed increment inbetween successive indices).
-The union of the corresponding elements is taken and
-passed along. Before anything else, the result set is replaced by its
-complement if 'I' is specified (for simple indices) or 'D' is specified
-(for domains). If there is both an index and a set spec string, the
-union of the results of both is taken and passed along. If the latter
-result is passed to either 'C' or 'R', it is replaced by its complement.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-A range is specified e.g. as <tt>10-14</tt> and it is inclusive, denoting
-in this case the indices <tt>{10,11,12,13,14}</tt>.
-</p>
-<p style="margin-bottom:0"><b>EXTENSION</b><br>
-The extension part is specified as
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>ext</b>( < <b>disc</b>(<i>k</i>) | <b>cdisc</b>(<i>k</i>) | <b>rdisc</b>(<i>k</i>) >)
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This option requires the input matrix to be held in memory. This implies it
-will not work with the <b>--from-disk</b> option.</p>
-<p style="margin-bottom:0" class="asd_par">
-This <i>assumes that the input matrix encodes a graph</i>, so the column
-and row domains must be equal.
-It will take the currently selected domain (column domain for
-<b>disc</b> and <b>cdisc</b>, row domain for <b>rdisc</b>), and add
-all nodes to it that are reachable in <i>k</i> steps.
-The <b>disc</b> variant replaces both column and row domains by
-the extended domain, the other variants just change a single domain.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Setting <i>k</i> to <tt>-1</tt> results in adding <i>all</i> nodes that
-can be reached from the start domain.
-</p>
-<p style="margin-bottom:0"><b>VALUES</b><br>
-The value part is specified as
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>val</b>(<tf-spec>)</p>
-<p style="margin-bottom:0" class="asd_par">
-It transforms or removes values according to <i><tf-spec></i>.
-Refer to <a class="local sibling" href="mcxio.html">mcxio</a> for a description of the transformation
-specification syntax and the available transformation primitives.</p>
-<p style="margin-bottom:0"><b>SIZE</b><br>
-The size part is specified as
-</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>size</b>( < <b>lt</b>(<i>x</i>) | <b>ceil</b>(<i>x</i>) | <b>gq</b>(<i>x</i>) | <b>rmgq</b>(<i>x</i>) > + )
-</p>
-<p style="margin-bottom:0" class="asd_par">
-Where <i>x</i> is a nonnegative integer, and multiple specifications
-are separated by commas.
-The strings 'lt', 'lq', 'gq', 'gt', respectively denote
-<i>less than</i>,
-<i>less than or equal to</i>,
-<i>greater than or equal to</i>,
-and
-<i>greater than</i>.
-</p>
-<p style="margin-bottom:0" class="asd_par">
-This prunes or removes column vectors based on their size. If <b>lt</b>
-is used, column vectors are removed if the number of entries exceeds
-the specified bound. If <b>gq</b> is used, vectors are discarded
-if the number of entries is smaller than the specified bound. If a column
-vector has an excess of entries over the bound specified by <b>ceil</b>, the
-smallest entries are removed. Ties are not arbitrarily broken, implying that
-the resulting vector may still have more entries than the specified bound.</p>
-<p style="margin-bottom:0"><b>FINALIZE</b><br>
-The finalize part is specified as
-<b>fin</b>( < <i>key</i> > )
-where <i>key</i> is a string and multiple keys are separated by commas. The
-corresponding actions are generally applied to the matrix that was extracted
-according to the domain and value specifications. Exceptions are indicated
-below. Currently, there is a fixed order in which actions are considered,
-corresponding with the order in which they are listed below.
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " >skel</div></div>
-<div class=" item_text " style="margin-left:2em">
-This creates an empty submatrix on the specified domains, and does
-<i>not</i> fill it with the corresponding entries from the
-<a class="intern" href="#opt-imx">source matrix</a>.
-Options from the <b>fin</b> part that affect the column and
-row domains of a matrix will still be in effect.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" >uni</div><div class=" item_cascade item_leftalign nowrap" >unir</div><div class=" item_cascade item_leftalign nowrap" >unic</div>
-<div class=" item_text " style="margin-left:2em">
-After the submatrix is selected from the source matrix, its domains
-are changed to mirror one or both of the domains of the source matrix.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >tp</div></div>
-<div class=" item_text " style="margin-left:2em">
-The resulting submatrix is replaced by its transpose.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " >cc</div></div>
-<div class=" item_text " style="margin-left:2em">
-The resulting submatrix is made characteristic.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" >scrubc</div><div class=" item_cascade item_leftalign nowrap" >scrubr</div><div class=" item_cascade item_leftalign nowrap" >scrubg</div><div class=" item_cascade item_leftalign nowrap" >scrub</div>
-<div class=" item_text " style="margin-left:2em">
-Domains are shrunk if there are no corresponding entries in the matrix.
-This is done for both domains if <tt>scrub</tt> is specified, for the
-column domain if <tt>scrubc</tt> is specified, and for the row domain
-if <tt>scrubr</tt> is specified. Thus, with <tt>scrubc</tt> columns are removed
-from the domain and the matrix if they are empty.
-With <tt>scrubg</tt> the union of the resulting domains is taken.
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" >mapc</div><div class=" item_cascade item_leftalign nowrap" >mapr</div><div class=" item_cascade item_leftalign nowrap" >map</div>
-<div class=" item_text " style="margin-left:2em">
-The appropriate domains are mapped onto consecutive indices starting at zero.
-</div>
-</div>
-<p style="margin-bottom:0"><b>OUTPUT</b><br>
-The output part is specified as
-<b>out</b>( <i>fname</i> <, <i>key</i> >* )
-that is, the <i>fname</i> option is obligatory if the <b>out</b> part is specified.
-Currently, key can be a single directive, namely <b>wb</b> specifying that
-the resulting matrix should be output in binary format.
-</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen.
-</p>
-
-<a name="seealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcx.html">mcx</a>,
-and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
-and the utilities in the mcl family.
-</p>
-</body>
-</html>
diff --git a/doc/mcxsubs.ps b/doc/mcxsubs.ps
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diff --git a/doc/tingea.log.html b/doc/tingea.log.html
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-<title>How to set the Tingea log parameters</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="tingea.log.ps"><b>tingea.log</b></a>
-14-137
-</p>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-tingea.log — How to set the Tingea log parameters</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-The Tingea logging framework is part of the Tingea library.
-In this context logging means that a pgrogram issues statements
-about what it is doing. It can do so for different purposes
-and at different levels of verbosity. By default logging statements
-are written on STDERR.</p>
-<p style="margin-bottom:0" class="asd_par">
-Tingea logging provides a quick and easy way for programmers to associate
-verbosity levels with logging statements.
-Only logging statements for which the verbosity
-level does not exceed the user-imposed threshold will be executed.
-Users can easily regulate the verbosity level by setting the environment
-variable TINGEA_LOG_TAG.
-Alternatively, programs may accept a command line argument.
-The format accepted by both environment variable and command line argument
-is identical.
-For the command line the programmer is free in choosing the option name.
-It is customarily named <b>-q</b>.
-The availability of such an option may vary from program to program.
-However, any program that makes use of the Tingea logging facilities
-can be regulated with the TINGEA_LOG_TAG environment variable.
-If a <b>-q</b> type option is present and the environment variable
-is set, then the environment variable is interpreted first followed
-by the <b>-q</b> argument.</p>
-<p style="margin-bottom:0" class="asd_par">
-Tingea logging allows a programmer to assign categories to logging
-statements. The categories FUNCTION and DATA have a subdivision
-ranging from fine-grained to coarse-grained. The categorie MONITORING has
-a subdivision ranging from low priority to high priority.
-The other categories are unimodal. These are IO, THREAD, PROCESS,
-and GAUGE. Three unspecified unimodal categories are SLOT1, SLOT2,
-and SLOT3. They can be used to encode program-specific semantics.</p>
-<p style="margin-bottom:0" class="asd_par">
-The programmer may assign multiple categories to a single logging statement.
-It is unusual for more than two categories to be specified. For example, IO
-and DATA at the LIST level may be combined to indicate a logging statement
-that provides data summaries for a certain IO related information. In order
-of granularity the DATA levels are CELL, LIST, and AGGREGRATE. If the user
-accepts IO logging and accepts DATA logging at level CELL or LIST the
-statement will be executed. If no IO logging is accepted or DATA logging is
-only accepted at the AGGREGRATE level, the statement will be skipped.</p>
-<p style="margin-bottom:0" class="asd_par">
-By default, all categories that are specified by the programmer need
-to pass the threshold specified by the user for that category.
-The user may relax this requirement so that only one category needs
-to pass the user threshold. In the above example, the statement
-categorized as both IO and DATA at LIST level will be accepted
-if the user specifies IO and DATA at AGGR level with OR semantics.</p>
-
-<a name="syntax"></a>
-<h2>SYNTAX</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-The syntax of the TINGEA_LOG_TAG environment variable is described by</p>
-<div class="verbatim"> [[189x]]{<[dfgimpstABC][1-9]>*,[V]}</div>
-<p style="margin-top:0em; margin-bottom:0em">
-which translates to the following. An optional lead tag is followed
-by a concatenation of units. A unit is either a pair in
-<tt>[dfgimpstABC] x [1-9x]</tt> or the single character <tt>V</tt>.
-The leading tag semantics are described further below.
-The single character <tt>V</tt>, if present, specifies that OR semantics
-should be used rather than the default AND semantics. The semantics
-for the other units are given below.</p>
-<div class="verbatim"> d DATA
- 1 CELL
- 2 LIST
- 3 AGGR
- x turned off
-
- f FUNCTION
- 1 LINE
- 2 FUNCTION
- 3 MODULE
- 4 APPLICATION
- x turned off
-
- m MONITORING
- 1 DEBUG
- 2 INFO
- 3 WARNING
- 4 ERROR
- 5 PANIC
- x turned off
-
- g GAUGE |
- i IO |
- n NETWORK |
- p PROCESS | (Inter Process really)
- t THREAD |______ 1 on
- | x off
- A SLOT1 |
- B SLOT2 |
- C SLOT3 |</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The leading tag can be used to set levels for all categories at once.
-Subsequent units may then alter this intial setting.
-The lead tag settings and their meaning are these:</p>
-<div class="verbatim"> 1 d1f1m1g1i1p1s1t1A1B1C1 # very yappy
- 9 d3f4m5gxixpxsxtxAxBxCx # very terse, only d f m
- 8 d3f4m5g1i1p1s1t1A1B1C1 # less terse
- x dxfxmxgxixpxsxtxAxBxCx # silent</div>
-<p style="margin-top:0em; margin-bottom:0em">
-All categories accept values between <tt>1</tt> and <tt>9</tt> in addition to the
-value <tt>x</tt>. As seen above, only a few categories contain more than
-one level and no category contains more than five levels.
-The rule is that if a level exceeds the maximul level available for a category
-it is simply interpreted as the maximum level.</p>
-<p style="margin-bottom:0" class="asd_par">
-The GAUGE category, if set, indicates that a program may write line based
-progress bars or other output in which a single line is accumulated over
-multiple statements. This implies that a single GAUGE logging statement may
-not result in newline-terminated output. This is undesirable in case the
-logging stream is directed to a file that is written to by other
-applications as well. In that case, turn off GAUGE. All other categories are
-garantueed to result in line-terminated output, by virtue of the programmer
-contract.</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-Stijn van Dongen.</p>
-</body>
-</html>
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-
-v_0 0.6 shn v_1 0.6 shn v_2 0.6 shn v_3 0.6 shn v_4 0.7 shn v_5 0.6 shn v_6 0.6
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-v_148 0.6 shn v_149 0.7 shn grestore
-
-% iterand6
-
-hdist 0 translate
-gsave
-scalef scalef -1 mul scale
-
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-
-%iterand12
-
-hdist -1 mul vdist -1 mul translate
-gsave
-scalef scalef -1 mul scale
-
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-
-%iterand26
-
-hdist 0 translate
-gsave
-scalef scalef -1 mul scale
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diff --git a/img/falkner-bidi.ps b/img/falkner-bidi.ps
deleted file mode 100644
index 2806694..0000000
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-
-shownodes 1 eq {
-v0 0.91 shn
-v1 0.97 shn
-v2 0.95 shn
-v3 0.91 shn
-v4 0.95 shn
-v5 0.93 shn
-v6 0.93 shn
-v7 1.00 shn
-v8 0.83 shn
-v9 0.91 shn
-v10 1.07 shn
-v11 1.07 shn
-v12 1.00 shn
-v13 0.95 shn
-v14 0.98 shn
-v15 1.14 shn
-v16 1.18 shn
-v17 1.09 shn
-v18 1.13 shn
-v19 1.20 shn
-v20 1.09 shn
-v21 1.03 shn
-v22 1.06 shn
-v23 0.88 shn
-v24 1.06 shn
-v25 1.16 shn
-v26 1.11 shn
-v27 0.92 shn
-v28 0.88 shn
-v29 0.99 shn
-v30 1.03 shn
-v31 1.01 shn
-v32 0.97 shn
-v33 1.00 shn
-v34 0.97 shn
-v35 0.99 shn
-v36 0.88 shn
-v37 0.94 shn
-v38 0.92 shn
-v39 0.95 shn
-v40 1.05 shn
-v41 1.03 shn
-v42 1.10 shn
-v43 1.01 shn
-v44 0.88 shn
-v45 0.98 shn
-v46 0.94 shn
-v47 1.07 shn
-v48 1.04 shn
-v49 0.87 shn
-v50 0.94 shn
-v51 0.83 shn
-v52 0.99 shn
-v53 0.97 shn
-v54 1.06 shn
-v55 1.03 shn
-v56 0.95 shn
-v57 1.04 shn
-v58 1.06 shn
-v59 0.93 shn
-v60 1.11 shn
-v61 1.08 shn
-v62 1.17 shn
-v63 0.96 shn
-v64 0.95 shn
-v65 1.08 shn
-v66 1.07 shn
-v67 1.02 shn
-v68 1.04 shn
-v69 1.09 shn
-v70 0.91 shn
-v71 0.89 shn
-v72 1.06 shn
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-v74 0.99 shn
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-v80 1.10 shn
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-v87 0.89 shn
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-v89 0.95 shn
-v90 0.88 shn
-v91 1.07 shn
-v92 1.10 shn
-v93 0.96 shn
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-v96 1.03 shn
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-v99 1.02 shn
-v100 1.11 shn
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-v105 0.96 shn
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-v108 0.87 shn
-v109 0.93 shn
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-v111 1.12 shn
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-v128 0.96 shn
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-v144 0.96 shn
-v145 0.89 shn
-v146 0.92 shn
-v147 0.90 shn
-v148 0.92 shn
-v149 0.87 shn
-} if
-
-/caption () def
-showpage
diff --git a/img/falkner.ps b/img/falkner.ps
deleted file mode 100644
index b445d18..0000000
--- a/img/falkner.ps
+++ /dev/null
@@ -1,678 +0,0 @@
-%!
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-
-% Old, scaling 10. BoundingBox: 206 205 394 394
-
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-/vertex_border_width 0.05 def
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-/BBLL [ 205 205 ] def
-/BBUR [ 385 385 ] def
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-B_test 1 eq { newpath
- BBLL aload pop moveto
- BBLL aload pop BBUR aload pop pop exch lineto % this is LR
- BBUR aload pop lineto
- BBUR aload pop BBLL aload pop pop exch lineto % this is UL
- closepath stroke
-} if
-
-
-50 200 translate
-25 25 scale
-
-/radius 0.24 def
-
-/proc_circle {
- gsave %% newpath moveto
- setgray
- aload pop moveto
- % 0.5 0.5 rmoveto
- currentpoint
- gsave
- currentpoint radius 0 360 arc
- fill
- grestore
- newpath radius 0 360 arc
- 0.0 setgray
- vertex_border_width setlinewidth
- stroke
- grestore
-} def
-
-/proc_line {
- gsave
- edge_width setlinewidth
- setgray
- aload pop moveto
- aload pop lineto
- stroke
- grestore
-} def
-
-/e {proc_line} def
-/n {proc_circle} def
-
-/unitx 1 def
-/unity 1 def
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-/v10[4 18]def/v11[6 18]def/v12[7 18]def/v13[11 18]def/v14[15 18]def
-/v15[16 18]def/v16[17 18]def/v17[4 17]def/v18[5 17]def/v19[6 17]def
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-/v35[18 16]def/v36[19 16]def/v37[4 15]def/v38[5 15]def/v39[8 15]def
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-0.544925 n v5 0.541982 n v6 0.570532 n v7 0.472799 n v8 0.659760
-n v9 0.576977 n v10 0.422198 n v11 0.437913 n v12 0.483941 n v13
-0.552187 n v14 0.532198 n v15 0.375332 n v16 0.344589 n v17
-0.407450 n v18 0.385459 n v19 0.346427 n v20 0.419215 n v21
-0.473870 n v22 0.471713 n v23 0.621629 n v24 0.431294 n v25
-0.361226 n v26 0.390696 n v27 0.548887 n v28 0.609660 n v29
-0.507276 n v30 0.471835 n v31 0.473967 n v32 0.521125 n v33
-0.548897 n v34 0.519209 n v35 0.507721 n v36 0.631548 n v37
-0.558457 n v38 0.567272 n v39 0.553632 n v40 0.446232 n v41
-0.489190 n v42 0.422871 n v43 0.455099 n v44 0.627956 n v45
-0.501296 n v46 0.545298 n v47 0.436983 n v48 0.485497 n v49
-0.629199 n v50 0.558145 n v51 0.776337 n v52 0.508481 n v53
-0.520576 n v54 0.439350 n v55 0.458171 n v56 0.565300 n v57
-0.483444 n v58 0.463721 n v59 0.545155 n v60 0.369783 n v61
-0.416384 n v62 0.346287 n v63 0.506732 n v64 0.551255 n v65
-0.394047 n v66 0.438288 n v67 0.506858 n v68 0.424081 n v69
-0.405122 n v70 0.639217 n v71 0.652449 n v72 0.396755 n v73
-0.354777 n v74 0.522318 n v75 0.476351 n v76 0.614533 n v77
-0.541569 n v78 0.481495 n v79 0.498663 n v80 0.407954 n v81
-0.519132 n v82 0.566577 n v83 0.485387 n v84 0.567410 n v85
-0.424921 n v86 0.474802 n v87 0.615930 n v88 0.441617 n v89
-0.553047 n v90 0.601098 n v91 0.442251 n v92 0.431175 n v93
-0.555504 n v94 0.490444 n v95 0.399644 n v96 0.497917 n v97
-0.481794 n v98 0.546625 n v99 0.474713 n v100 0.396048 n v101
-0.423658 n v102 0.569271 n v103 0.500285 n v104 0.494140 n v105
-0.532968 n v106 0.387508 n v107 0.496152 n v108 0.692670 n v109
-0.558109 n v110 0.521170 n v111 0.395399 n v112 0.594159 n v113
-0.393716 n v114 0.410750 n v115 0.592390 n v116 0.511143 n v117
-0.460369 n v118 0.557301 n v119 0.421122 n v120 0.510552 n v121
-0.573567 n v122 0.441674 n v123 0.477888 n v124 0.421878 n v125
-0.383757 n v126 0.388152 n v127 0.506438 n v128 0.585930 n v129
-0.490773 n v130 0.437226 n v131 0.389423 n v132 0.394569 n v133
-0.532359 n v134 0.424528 n v135 0.427765 n v136 0.675898 n v137
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-0.595409 n v146 0.594567 n v147 0.585015 n v148 0.555668 n v149
-0.617555 n
-
-/Times-Bold findfont
-0.5 scalefont
-setfont
-
-
-/proc_show {
-aload pop moveto rmoveto show
-} def
-
-(0) -0.5 0.3 v0 proc_show
-(1) -0.5 0.3 v1 proc_show
-(2) -0.5 0.3 v2 proc_show
-(3) -0.5 0.3 v3 proc_show
-(4) -0.5 0.3 v4 proc_show
-(5) -0.5 0.3 v5 proc_show
-(6) -0.5 0.3 v6 proc_show
-(7) -0.5 0.3 v7 proc_show
-(8) -0.5 0.3 v8 proc_show
-(9) -0.5 0.3 v9 proc_show
-(11) -0.3 0.3 v11 proc_show
-(12) 0.3 -0.2 v12 proc_show
-(13) 0.4 -0.1 v13 proc_show
-(14) -0.5 0.3 v14 proc_show
-(16) 0.2 -0.1 v16 proc_show
-(17) -0.8 -0.1 v17 proc_show
-(18) -0.2 -0.7 v18 proc_show
-(19) -0.2 -0.7 v19 proc_show
-(20) -0.2 -0.7 v20 proc_show
-(21) 0.2 0.1 v21 proc_show
-(22) -0.8 0.1 v22 proc_show
-(23) -0.5 0.3 v23 proc_show
-(25) -0.2 -0.7 v25 proc_show
-(26) 0.0 0.3 v26 proc_show
-(27) 0.2 0.3 v27 proc_show
-(28) -0.5 0.3 v28 proc_show
-(29) -0.5 0.3 v29 proc_show
-(30) -1.0 -0.1 v30 proc_show
-(31) -0.1 0.3 v31 proc_show
-(32) 0.3 -0.4 v32 proc_show
-(33) -0.2 -0.7 v33 proc_show
-(34) 0.3 -0.4 v34 proc_show
-(35) -0.2 -0.7 v35 proc_show
-(36) 0.3 -0.4 v36 proc_show
-(37) -0.6 0.3 v37 proc_show
-(38) 0.4 -0.1 v38 proc_show
-(39) -0.8 -0.1 v39 proc_show
-(40) 0.2 0.1 v40 proc_show
-(41) -0.8 0.1 v41 proc_show
-(42) 0.3 -0.3 v42 proc_show
-(43) -0.8 -0.1 v43 proc_show
-(44) -0.8 -0.1 v44 proc_show
-(45) -0.2 -0.6 v45 proc_show
-(46) -0.2 -0.6 v46 proc_show
-(47) -0.8 -0.4 v47 proc_show
-(48) 0.2 0.1 v48 proc_show
-(49) 0.4 -0.1 v49 proc_show
-(50) 0.4 -0.1 v50 proc_show
-(51) -0.8 -0.1 v51 proc_show
-(52) 0.4 -0.1 v52 proc_show
-(53) -0.8 -0.1 v53 proc_show
-(54) -0.2 -0.7 v54 proc_show
-(55) -0.2 0.3 v55 proc_show
-(56) -0.8 0.1 v56 proc_show
-(57) -0.3 0.3 v57 proc_show
-(59) 0.2 0.3 v59 proc_show
- (58) 1.2 0.3 v59 proc_show
-(60) -0.5 0.3 v60 proc_show
-(62) -0.5 0.3 v62 proc_show
-(63) -0.5 0.3 v63 proc_show
-(64) 0.4 -0.1 v64 proc_show
-(65) -0.8 -0.3 v65 proc_show
-(66) 0.4 -0.1 v66 proc_show
-(67) 0.4 -0.1 v67 proc_show
-(68) -0.8 -0.1 v68 proc_show
-(69) 0.5 -0.2 v69 proc_show
-(70) 0.2 0.1 v70 proc_show
-(71) -0.8 0.1 v71 proc_show
-(72) -0.8 -0.1 v72 proc_show
-(74) 0.3 -0.1 v74 proc_show
-(75) 0.4 -0.1 v75 proc_show
-(76) -0.8 -0.1 v76 proc_show
-(77) 0.4 -0.1 v77 proc_show
-(78) -0.8 -0.2 v78 proc_show
-(79) -1.1 -0.1 v79 proc_show
-(80) 0.3 0.1 v80 proc_show
-(81) -0.3 0.3 v81 proc_show
-(82) 0.4 -0.1 v82 proc_show
-(83) 0.3 -0.2 v83 proc_show
-(84) -0.8 -0.1 v84 proc_show
-(85) 0.4 -0.1 v85 proc_show
-(86) 0.4 -0.1 v86 proc_show
-(87) -0.8 -0.1 v87 proc_show
-(88) 0.3 -0.2 v88 proc_show
-(89) 0.3 -0.3 v89 proc_show
-(90) -0.8 -0.1 v90 proc_show
-(92) 0.4 -0.1 v92 proc_show
-(93) -0.2 -0.6 v93 proc_show
-(94) -0.6 -0.6 v94 proc_show
-(95) 0.1 -0.7 v95 proc_show
-(96) -0.3 -0.7 v96 proc_show
-(97) 0.3 -0.4 v97 proc_show
-(98) 0.3 -0.3 v98 proc_show
-(99) -0.8 -0.1 v99 proc_show
-(101) 0.2 0.1 v101 proc_show
-(102) 0.3 -0.4 v102 proc_show
-(103) -0.4 -0.6 v103 proc_show
-(104) 0.3 -0.3 v104 proc_show
-(105) 0.5 -0.3 v105 proc_show
-(106) -1.1 -0.1 v106 proc_show
-(107) 0.2 -0.2 v107 proc_show
-(108) -1.1 -0.1 v108 proc_show
-(109) -1.1 -0.2 v109 proc_show
-(110) -1.1 -0.1 v110 proc_show
-(111) 0.3 -0.2 v111 proc_show
-(112) -1.1 -0.1 v112 proc_show
-(114) 0.3 -0.2 v114 proc_show
-(115) 0.3 -0.2 v115 proc_show
-(116) 0.3 -0.2 v116 proc_show
-(117) -1.1 -0.1 v117 proc_show
-(118) -0.4 -0.6 v118 proc_show
-(120) 0.3 -0.2 v120 proc_show
-(121) 0.3 -0.2 v121 proc_show
-(122) -1.1 -0.1 v122 proc_show
-(123) -0.5 0.3 v123 proc_show
-(124) 0.3 -0.2 v124 proc_show
-(125) -1.1 -0.1 v125 proc_show
-(126) -0.4 -0.6 v126 proc_show
-(127) 0.3 -0.2 v127 proc_show
-(128) -1.1 -0.1 v128 proc_show
-(129) -1.1 -0.1 v129 proc_show
-(130) -1.1 -0.1 v130 proc_show
-(132) 0.0 0.3 v132 proc_show
-(133) 0.1 0.2 v133 proc_show
-(134) -1.0 0.1 v134 proc_show
-(135) 0.1 -0.5 v135 proc_show
-(136) 0.1 -0.5 v136 proc_show
-(137) 0.3 -0.2 v137 proc_show
-(138) -1.1 -0.1 v138 proc_show
-(139) -0.4 -0.6 v139 proc_show
-(141) 0.3 -0.2 v141 proc_show
-(142) -1.1 -0.1 v142 proc_show
-(143) -1.1 -0.1 v143 proc_show
-(144) 0.3 -0.2 v144 proc_show
-(145) -1.1 -0.1 v145 proc_show
-(146) -0.4 -0.6 v146 proc_show
-(147) -0.4 -0.6 v147 proc_show
-(148) -0.6 -0.6 v148 proc_show
-(149) -0.2 -0.6 v149 proc_show
-
-showpage
diff --git a/img/small.ps b/img/small.ps
deleted file mode 100644
index 74dabe7..0000000
--- a/img/small.ps
+++ /dev/null
@@ -1,162 +0,0 @@
-%!
-%%BoundingBox: 102 200 410 405
-
-/B_test 1 def % set to 1 to test BoundingBox parameters
-/BBLL [ 102 200 ] def
-/BBUR [ 410 405 ] def
-
-.5 setlinewidth
-
-% remark: The drawing points are defined in terms of unitx and unity. Why not
-% scale the whole thing after drawing it? My reason for this is that labels
-% which are drawn next to the nodes, and spacing between labels and nodes,
-% generally must not be scaled accordingly. I am currently not aware of other
-% solutions to this small problem.
-
-
-/unitx 3 def
-/unity 3 def
-/unithx unitx 2 div def
-/unithy unity 2 div def
-/radius unitx .6666666 mul def
-
-/proc_scale {
- unity mul exch unitx mul exch
-} def
-
-/proc_showpoint {
- aload pop moveto proc_circle
-} def
-
-/proc_circle {
- gsave currentpoint radius 0 360 arc
- 0 setgray fill grestore
-} def
-
-B_test 1 eq { newpath
- BBLL aload pop moveto
- BBLL aload pop BBUR aload pop pop exch lineto % this is LR
- BBUR aload pop lineto
- BBUR aload pop BBLL aload pop pop exch lineto % this is UL
- closepath stroke
-} if
-
-2 2 scale
-0 30 translate
-
-/v_0 [ 30 30 ] def
-/v_1 [ 40 30 ] def
-/v_2 [ 45 30 ] def
-/v_3 [ 55 30 ] def
-
-/v_4 [ 42.5 35 ] def
-
-/v_5 [ 22.5 40 ] def
-/v_6 [ 37.5 40 ] def
-/v_7 [ 47.5 40 ] def
-/v_8 [ 62.5 40 ] def
-
-/v_9 [ 30 50 ] def
-/v_10 [ 55 50 ] def
-/v_11 [ 62.5 50 ] def
-
-/c1_3_10 [ 56 36 ] def
-/c2_3_10 [ 56 44 ] def
-
-/c1_7_8 [51 41 ] def
-/c2_7_8 [59 41 ] def
-
-
-/nodes [v_0 v_1 v_2 v_3 v_4 v_5 v_6 v_7 v_8 v_9 v_10 v_11] def
-/edge1 [
- [v_0 v_1]
- [v_0 v_5]
- [v_0 v_6]
- [v_0 v_9]
- [v_1 v_2]
- [v_1 v_4]
- [v_2 v_3]
- [v_2 v_4]
- [v_3 v_7]
- [v_3 v_10]
- [v_3 v_8]
- [v_4 v_6]
- [v_4 v_7]
- [v_5 v_9]
- [v_6 v_9]
- [v_7 v_10]
- [v_7 v_8]
- [v_8 v_10]
- [v_8 v_11]
- [v_10 v_11]
-] def
-
-newpath
-nodes {
-aload pop proc_scale moveto proc_circle % load array values, scale, and circle
-} forall
-
-edge1 {
-newpath
-aload pop % load array which consists of two nodes which are again arrays..
-aload pop proc_scale moveto % load first node.
-aload pop proc_scale lineto % load second node.
-stroke
-} forall
-
-/Times-Roman findfont
-8 scalefont
-setfont
-
-v_0 aload pop proc_scale moveto
-0 unitx 3 mul sub 0 unity 2 mul sub rmoveto
-(0) show
-
-v_1 aload pop proc_scale moveto
-0 unitx 2 mul sub 0 unity 3 mul sub rmoveto
-(1) show
-
-v_2 aload pop proc_scale moveto
-0 unitx 2 mul sub 0 unity 3 mul sub rmoveto
-(2) show
-
-v_3 aload pop proc_scale moveto
-0 unitx 2 mul sub 0 unity 3 mul sub rmoveto
-(3) show
-
-v_4 aload pop proc_scale moveto
-unitx 2 mul 0 unity sub rmoveto
-(4) show
-
-v_5 aload pop proc_scale moveto
-0 unitx 2 mul sub unity rmoveto
-(5) show
-
-v_6 aload pop proc_scale moveto
-unitx 1 mul unity rmoveto
-(6) show
-
-v_7 aload pop proc_scale moveto
-0 unitx 2 mul sub unity rmoveto
-(7) show
-
-v_8 aload pop proc_scale moveto
-unitx unity rmoveto
-(8) show
-
-v_9 aload pop proc_scale moveto
-0 unitx 2 mul sub unity 1.5 mul rmoveto
-(9) show
-
-v_10 aload pop proc_scale moveto
-0 unitx 2 mul sub unity 1.5 mul rmoveto
-(10) show
-
-v_11 aload pop proc_scale moveto
-0 unitx 2 mul sub unity 1.5 mul rmoveto
-(11) show
-
-
-
-showpage
-
diff --git a/include/Makefile.in b/include/Makefile.in
deleted file mode 100644
index 324c548..0000000
--- a/include/Makefile.in
+++ /dev/null
@@ -1,537 +0,0 @@
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-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
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-mclblastline.1: mclblastline.azm
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- $(ZOEM) -s $(zmmval) -i mclblastline -d roff -o mclblastline.1
-
-mclblastline.ps: mclblastline.1
- $(TROFF) -man mclblastline.1 > mclblastline.ps
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-
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-
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-mcxdeblast.ps: mcxdeblast.1
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-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/src/alien/oxygen/doc/mclblastline.1 b/src/alien/oxygen/doc/mclblastline.1
deleted file mode 100644
index f752cde..0000000
--- a/src/alien/oxygen/doc/mclblastline.1
+++ /dev/null
@@ -1,136 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mclblastline" 1 "16 May 2014" "mclblastline 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
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-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mclblastline \- a pipeline for clustering from BLAST files\&.
-.SH SYNOPSIS
-\fBmclblastline\fP file-name
-
-\fBmclblastline\fP [deblast options] [pipeline options] file-name
-
-\fBNOTE\fP
-.br
-\fBmcl\fP has acquired the ability to proceed from label input
-as produced by \fBmcxdeblast\fP\&. This enables a very lightweight
-mechanism of generating clusterings from BLAST files\&.
-You might want to use this mechanism,
-documented in the \fBmcl manual\fP\&.
-
-\fBNOTE\fP
-.br
-mclblastline used to require (given default parameters)
-the presence of the \fBzoem\fP macro processor to produce detailed output\&.
-This is no longer the case\&. By default mclblastline now creates
-a line-based tab-separated dump file\&.
-Zoem \fIwill\fP be invoked when the --fmt-fancy option is supplied\&.
-In that case, zoem obviously has to be installed\&.
-.SH DESCRIPTION
-\fBmclblastline\fP wraps around \fBmclpipeline\fP\&. It supplies the
-\fB--parser\fP=\fIapp\fP
-and \fB--parser-tag\fP=\fIstr\fP options, setting them respectively
-to \fImcxdeblast\fP and \fIblast\fP\&. This tells
-\fBmclpipeline\fP to use
-\fBmcxdeblast\fP as the parse script in its pipeline\&.
-The significance of
-the \fIblast\fP tag is that any mcxdeblast option can be passed through
-mclblastline and mclpipeline by inserting this tag into the option\&.
-For example, mcxdeblast accepts the \fB--score\fP=\fIx\fP option\&.
-When using mclblastline, you specify it as \fB--blast-score\fP=\fIx\fP\&.
-There are two exceptions to this rule, namely the
-\fB--xi-dat\fP=\fIstr\fP and \fB--xo-dat\fP=\fIstr\fP options\&. Refer to
-the \fBmclpipeline\fP manual for more information\&.
-
-Additionally, all mclpipeline options are acceptable to \fBmcxdeblast\fP as
-well\&. The \fB--whatif\fP is useful for getting a feel for the pipeline\&.
-The \fB--mcl-I\fP=\fIf\fP inflation option and \fB--mcl-scheme\fP=\fIi\fP scheme
-index options are your basic means for respectively manipulating cluster
-granularity and allocating resources\&. Read the \fBmcl\fP manual entries for
-a description of the corresponding \fB-I\fP and \fB-scheme\fP mcl
-options\&.
-
-The best advice is to glance over the \fBmcxdeblast\fP and \fBmclpipeline\fP
-options in order to get a feeling for which of those may come in handy for
-you\&. Then start experimenting\&. Use the \fB--whatif\fP option, it will
-tell you what would happen without actually doing it\&.
-.SH OPTIONS
-All \fBmcxdeblast\fP and \fBmclpipeline\fP options\&.
-mcxdeblast options must be passed using the mechanism described above\&.
-.SH EXAMPLES
-
-.nf \fC
- mclblastline --blast-score=b
- --blast-sort=a --blast-bcut=5 --mcl-I=2\&.5 myblastfile
-.fi \fR
-
-This will use bit scores, sort cluster indices such that the corresponding
-labels are ordered alphabetically, ignore bit scores not exceeding 5, and
-use inflation value 2\&.5\&. In this case, the output clustering will be in the
-file named \fCmyblastfile\&.I25s2\fP (I25 identifying the inflation value and s2
-identifying the resource scheme) and the formatted output will be in the
-file \fCmyblastfile\&.I25s2\&.fmt\fP\&.
-
-.nf \fC
- mclblastline --prepare-mcl myblastfile
- mclblastline --start-mcl --mcl-I=1\&.2 myblastfile
- mclblastline --start-mcl --mcl-I=1\&.6 myblastfile
- mclblastline --start-mcl --mcl-I=2\&.0 myblastfile
- mclblastline --start-mcl --mcl-I=2\&.4 myblastfile
- mclblastline --start-mcl --mcl-I=2\&.8 myblastfile
- etc \&.\&.
-.fi \fR
-
-The first run prepares an input matrix to be read by \fBmcl\fP\&.
-In this case its file will be named \fCmyblastfile\&.sym\fP\&.
-The subsequent runs use this matrix\&.
-\fBCAVEAT\fP there are some options that you need to repeat
-when executing such a resumed run\&. They are clearly marked
-in the \fBmclpipeline\fP manual - namely those options
-that affect names of (intermediate) files\&. Most importantly,
-this concerns the mclpipeline options that have prefix
-\fB--xo\fP or \fB--xi\fP\&. For example,
-
-.nf \fC
- mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1\&.2 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1\&.6 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.0 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.4 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.8 myblastfile
- etc \&.\&.
-.fi \fR
-
-In this case, the matrix file will be named \fCmyblastfile\&.b\&.sym\fP,
-and the \fB--xo-dat\fP options must be repeated in all runs
-so that the pipeline reconstructs the correct file name(s)\&.
-.SH AUTHOR
-
-Stijn van Dongen
-.SH SEE ALSO
-
-\fBmcxdeblast\fP, \fBmclpipeline\fP, \fBmcxassemble\fP\&.
diff --git a/src/alien/oxygen/doc/mclblastline.html b/src/alien/oxygen/doc/mclblastline.html
deleted file mode 100644
index 98fccac..0000000
--- a/src/alien/oxygen/doc/mclblastline.html
+++ /dev/null
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-</style>
-<title>The mclblastline manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mclblastline.ps"><b>mclblastline</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#examples">EXAMPLES</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#sealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mclblastline — a pipeline for clustering from BLAST files.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mclblastline</b> file-name</p>
-<p style="margin-bottom:0" class="asd_par">
-<b>mclblastline</b> [deblast options] [pipeline options] file-name</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-<b>mcl</b> has acquired the ability to proceed from label input
-as produced by <b>mcxdeblast</b>. This enables a very lightweight
-mechanism of generating clusterings from BLAST files.
-You might want to use this mechanism,
-documented in the <a class="local sibling" href="mcl.html">mcl manual</a>.</p>
-<p style="margin-bottom:0"><b>NOTE</b><br>
-mclblastline used to require (given default parameters)
-the presence of the <b>zoem</b> macro processor to produce detailed output.
-This is no longer the case. By default mclblastline now creates
-a line-based tab-separated dump file.
-Zoem <i>will</i> be invoked when the --fmt-fancy option is supplied.
-In that case, zoem obviously has to be installed.</p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-<b>mclblastline</b> wraps around <b>mclpipeline</b>. It supplies the
-<b>--parser</b>=<i>app</i>
-and <b>--parser-tag</b>=<i>str</i> options, setting them respectively
-to <i>mcxdeblast</i> and <i>blast</i>. This tells
-<a class="local sibling" href="mclpipeline.html">mclpipeline</a> to use
-<a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> as the parse script in its pipeline.
-The significance of
-the <i>blast</i> tag is that any mcxdeblast option can be passed through
-mclblastline and mclpipeline by inserting this tag into the option.
-For example, mcxdeblast accepts the <b>--score</b>=<i>x</i> option.
-When using mclblastline, you specify it as <b>--blast-score</b>=<i>x</i>.
-There are two exceptions to this rule, namely the
-<b>--xi-dat</b>=<i>str</i> and <b>--xo-dat</b>=<i>str</i> options. Refer to
-the <a class="local sibling" href="mclpipeline.html">mclpipeline</a> manual for more information.</p>
-<p style="margin-bottom:0" class="asd_par">
-Additionally, all mclpipeline options are acceptable to <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> as
-well. The <b>--whatif</b> is useful for getting a feel for the pipeline.
-The <b>--mcl-I</b>=<i>f</i> inflation option and <b>--mcl-scheme</b>=<i>i</i> scheme
-index options are your basic means for respectively manipulating cluster
-granularity and allocating resources. Read the <a class="local sibling" href="mcl.html">mcl</a> manual entries for
-a description of the corresponding <b>-I</b> and <b>-scheme</b> mcl
-options.</p>
-<p style="margin-bottom:0" class="asd_par">
-The best advice is to glance over the <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> and <a class="local sibling" href="mclpipeline.html">mclpipeline</a>
-options in order to get a feeling for which of those may come in handy for
-you. Then start experimenting. Use the <b>--whatif</b> option, it will
-tell you what would happen without actually doing it.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-All <a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> and <a class="local sibling" href="mclpipeline.html">mclpipeline</a> options.
-mcxdeblast options must be passed using the mechanism described above.</p>
-
-<a name="examples"></a>
-<h2>EXAMPLES</h2>
-<div class="verbatim"> mclblastline --blast-score=b
- --blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile</div>
-<p style="margin-top:0em; margin-bottom:0em">
-This will use bit scores, sort cluster indices such that the corresponding
-labels are ordered alphabetically, ignore bit scores not exceeding 5, and
-use inflation value 2.5. In this case, the output clustering will be in the
-file named <tt>myblastfile.I25s2</tt> (I25 identifying the inflation value and s2
-identifying the resource scheme) and the formatted output will be in the
-file <tt>myblastfile.I25s2.fmt</tt>.</p>
-<div class="verbatim"> mclblastline --prepare-mcl myblastfile
- mclblastline --start-mcl --mcl-I=1.2 myblastfile
- mclblastline --start-mcl --mcl-I=1.6 myblastfile
- mclblastline --start-mcl --mcl-I=2.0 myblastfile
- mclblastline --start-mcl --mcl-I=2.4 myblastfile
- mclblastline --start-mcl --mcl-I=2.8 myblastfile
- etc ..</div>
-<p style="margin-top:0em; margin-bottom:0em">
-The first run prepares an input matrix to be read by <b>mcl</b>.
-In this case its file will be named <tt>myblastfile.sym</tt>.
-The subsequent runs use this matrix.
-<b>CAVEAT</b> there are some options that you need to repeat
-when executing such a resumed run. They are clearly marked
-in the <a class="local sibling" href="mclpipeline.html">mclpipeline</a> manual - namely those options
-that affect names of (intermediate) files. Most importantly,
-this concerns the mclpipeline options that have prefix
-<b>--xo</b> or <b>--xi</b>. For example,</p>
-<div class="verbatim"> mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1.2 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=1.6 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.0 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.4 myblastfile
- mclblastline --start-mcl --xo-dat=b --mcl-I=2.8 myblastfile
- etc ..</div>
-<p style="margin-bottom:0" class="asd_par">
-In this case, the matrix file will be named <tt>myblastfile.b.sym</tt>,
-and the <b>--xo-dat</b> options must be repeated in all runs
-so that the pipeline reconstructs the correct file name(s).</p>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-<p style="margin-bottom:0" class="asd_par">
-Stijn van Dongen</p>
-
-<a name="sealso"></a>
-<h2>SEE ALSO</h2>
-<p style="margin-bottom:0" class="asd_par">
-<a class="local sibling" href="mcxdeblast.html">mcxdeblast</a>, <a class="local sibling" href="mclpipeline.html">mclpipeline</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>.</p>
-</body>
-</html>
diff --git a/src/alien/oxygen/doc/mclblastline.ps b/src/alien/oxygen/doc/mclblastline.ps
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diff --git a/src/alien/oxygen/doc/mcxdeblast.1 b/src/alien/oxygen/doc/mcxdeblast.1
deleted file mode 100644
index 335b4d7..0000000
--- a/src/alien/oxygen/doc/mcxdeblast.1
+++ /dev/null
@@ -1,193 +0,0 @@
-.\" Copyright (c) 2014 Stijn van Dongen
-.TH "mcxdeblast" 1 "16 May 2014" "mcxdeblast 14-137" "USER COMMANDS "
-.po 2m
-.de ZI
-.\" Zoem Indent/Itemize macro I.
-.br
-'in +\\$1
-.nr xa 0
-.nr xa -\\$1
-.nr xb \\$1
-.nr xb -\\w'\\$2'
-\h'|\\n(xau'\\$2\h'\\n(xbu'\\
-..
-.de ZJ
-.br
-.\" Zoem Indent/Itemize macro II.
-'in +\\$1
-'in +\\$2
-.nr xa 0
-.nr xa -\\$2
-.nr xa -\\w'\\$3'
-.nr xb \\$2
-\h'|\\n(xau'\\$3\h'\\n(xbu'\\
-..
-.if n .ll -2m
-.am SH
-.ie n .in 4m
-.el .in 8m
-..
-.SH NAME
-mcxdeblast \- parse BLAST files and stream
-output directly into mcl or write mcxassemble input\&.
-.SH SYNOPSIS
-\fBmcxdeblast\fP file-name
-
-\fBmcxdeblast\fP
-\fB[--score=\fP<b|e|r> (\fIbit scores|e-values|normalize bit score\fP)\fB]\fP
-\fB[--m9\fP (\fIexpect BLAST column format\fP)\fB]\fP
-\fB[--out\fP <fname> (\fIoutput file\fP)\fB]\fP
-\fB[--line-mode\fP abc (\fIwrite ID1 ID2 score format\fP)\fB]\fP
-\fB[--sort=\fP<a|o> (\fIalphabetic|occurrence sorting\fP)\fB]\fP
-\fB[--xi-dat=\fP<suf> (\fIstrip <suf> from file-name\fP)\fB]\fP
-\fB[--xo-dat=\fP<suf> (\fIadd <suf> to base name\fP)\fB]\fP
-\fB[--bcut=\fP<val> (\fIbit score cutoff\fP)\fB]\fP
-\fB[--ecut=\fP<val> (\fIE-value cutoff\fP)\fB]\fP
-\fB[--rcut=\fP<val> (\fIraw value cutoff\fP)\fB]\fP
-\fB[--tab=\fP<fname> (\fItab file\fP)\fB]\fP
-<file-name>
-.SH DESCRIPTION
-
-\fBmcxdeblast\fP parses BLAST files\&.
-
-In \fIstream mode\fP mcxdeblast output can be directly streamed to mcl by
-using the mcxdeblast \fB--line-mode\fP=\fIabc\fP option and equipping mcl with
-either \fB--abc\fP or \fB--expect-abc\fP\&. This can be considered the
-easy, lightweight and fast track\&. This functionality was recently acquired
-by mcl\&.
-
-In the classic and slightly more heavy-handed \fIassemble mode\fP, mcxdeblast
-creates output files suitable for use by mcxassemble\&. The latter can in
-turn create input suitable for mcl\&. This is the mode in which mcxdeblast is
-employed by \fBmclblastline\fP\&.
-.SH STREAM MODE
-Enter stream mode by specifiying \fB--line-mode\fP=\fIabc\fP\&.
-Use \fB--m9\fP if the input is in columnar output\&. Pipe the result
-to a file or directly to mcl\&. Example invocations can be found
-in \fBthe mcl manual\fP\&.
-.SH ASSEMBLE MODE
-If the input file is named \fCiput\fP, mcxdeblast will by
-default create files \fCiput\&.hdr\fP, \fCiput\&.raw\fP, \fCiput\&.tab\fP,
-\fCiput\&.map\fP, and \fCiput\&.err\fP\&. The \fChdr\fP file contains
-information about the number of nodes found\&. It will be read
-by \fBmcxassemble\fP\&. The \fCraw\fP file contains the co-occurrence
-scores between different nodes (peptides), also to be
-read by mcxassemble\&. The co-occurrence scores are in
-terms of mcl indentiers, which are subjected to rearranging
-by mcxassemble in order to correctly align them with the tab file\&.
-The \fCtab\fP file contains bindings between mcl identifiers
-(after rearranging as specified in the map file) and the BLAST labels
-(peptide identifiers)\&. Refer to the manual of \fBmcxassemble\fP
-for the syntax of a tab file\&.
-The \fCerr\fP file contains a list of any errors encountered\&.
-
-If the \fB--tab\fP=\fBfname\fP option is used mcxdeblast changes
-its behaviour\&. It will read the file \fBfname\fP, and use
-the bindings found therein\&. It will no longer output any
-of the \fChdr\fP, \fCmap\fP, or \fCtab\fP files\&. The \fChdr\fP
-file should be provided by the same application that generated
-the specified tab file, and the \fCmap\fP file should no longer be
-necessary (it might be convenient though and perhaps the
-future will bring a new \fB--map\fP option)\&.
-
-The \fB--tab\fP=\fBfname\fP option can be convenient e\&.g\&. if
-you split a BLAST job over multiple machines and want
-to apply mcxdeblast to each of the subresults\&. You do
-this by generating a single central tab file in advance\&.
-Then provide each instance of mcxdeblast with this tab file\&.
-Each instance will generate a \fCraw\fP file\&. The respective
-\fCraw\fP files can simply be concatenated and fed to mcxassemble
-using its \fB-raw\fP option\&. Additionally, a \fChdr\fP file
-has to be specified for mcxassemble using its \fB-hdr\fP
-option\&. The syntax of \fChdr\fP files is described in
-the \fBmcxassemble\fP manual\&.
-Currently there is usually only one variable
-in the \fChdr\fP file, which is the number of bindings
-listed in the tab file\&. This number, in turn, should equal
-the total number of different peptides encountered in the BLAST input\&.
-.SH OPTIONS
-
-.ZI 2m "\fB--tab\fP=<fname> (\fItab file\fP)"
-\&
-.br
-Specify a tab file to use, rather than automatically generating one\&.
-.in -2m
-
-.ZI 2m "\fB--out\fP <fname> (\fIoutput file\fP)"
-\&
-.br
-Specify the name for the output file\&.
-.in -2m
-
-.ZI 2m "\fB--score\fP=<b|e|r> (\fIbit scores|e-values|norm bit score\fP)"
-\&
-.br
-Specify whether to use bit scores, E-values, or bit scores
-normalized by length of the HSP\&.
-.in -2m
-
-.ZI 2m "\fB--sort\fP=<a|o> (\fIalphabetic|occurrence sorting\fP)"
-\&
-.br
-Specify how to sort labels\&.
-.in -2m
-
-.ZI 2m "\fB--m9\fP (\fIexpect BLAST column format\fP)"
-\&
-.br
-Use this option to parse BLAST output formatted with the -m 9 option\&.
-.in -2m
-
-.ZI 2m "\fB--line-mode\fP=abc (\fIwrite ID1 ID2 SCORE format\fP)"
-\&
-.br
-Use this to stream output directly into mcl\&. Here \fCabc\fP
-is a literal; \fB--line-mode\fP may acquire other line output
-modes\&.
-.in -2m
-
-.ZI 2m "\fB--xi-dat\fP=<suf> (\fIstrip <suf> from <file-name>\fP)"
-\&
-.br
-If set, the suffix <suf> is stripped from file-name in order
-to obtain the base name for output\&. If <file-name> does not
-end with suffix, it is assumed to be the base name, and <suf> is
-added in order to obtain the (real) file-name\&.
-.in -2m
-
-.ZI 2m "\fB--xo-dat\fP=<suf> (\fIadd <suf> to base name\fP)"
-\&
-.br
-Attaches the suffix to the base name\&. Use this to distinguish
-between different parses\&. One might for example
-use \fB--score\fP=\fIb\fP \fB--bcut\fP=\fI5\fP \fB--xo-dat\fP=\fIb\fP\&.
-.in -2m
-
-.ZI 2m "\fB--bcut\fP=<val> (\fIbit score cutoff\fP)"
-\&
-.br
-Bit scores below the cutoff value are ignored\&. This
-triggers the output of bit scores and ignores all other values\&.
-.in -2m
-
-.ZI 2m "\fB--ecut\fP=<val> (\fIE-value cutoff\fP)"
-\&
-.br
-E-values below the cutoff value are ignored\&. This triggers
-the output of E-values and ignores all other values\&.
-.in -2m
-
-.ZI 2m "\fB--rcut\fP=<val> (\fIraw value cutoff\fP)"
-\&
-.br
-Raw values below the cutoff value are ignored\&. This
-triggers the output of raw values and ignores all other values\&.
-.in -2m
-.SH AUTHOR
-Stijn van Dongen\&.
-Jason Stajich implemented the \fB--m9\fP option\&.
-Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments
-and fixes\&.
-.SH SEE ALSO
-\fBmclblastline\fP, \fBmcxassemble\fP, \fBmcl\fP,
-\fBclmformat\fP\&.
diff --git a/src/alien/oxygen/doc/mcxdeblast.html b/src/alien/oxygen/doc/mcxdeblast.html
deleted file mode 100644
index 7d5066c..0000000
--- a/src/alien/oxygen/doc/mcxdeblast.html
+++ /dev/null
@@ -1,303 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<!-- Copyright (c) 2014 Stijn van Dongen -->
-<head>
-<meta name="keywords" content="manual">
-<style type="text/css">
-/* START aephea.base.css */
-body
-{ text-align: justify;
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-a:link { text-decoration: none; }
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-a.intern:link { color: #1111aa; }
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-a.extern:link { color: #aa1111; }
-a.extern:active { color: #aa1111; }
-a.extern:visited { color: #661111; }
-a.quiet:link { color: black; }
-a.quiet:active { color: black; }
-a.quiet:visited { color: black; }
-div.verbatim
-{ font-family: monospace;
-margin-top: 1em;
-margin-bottom: 1em;
-font-size: 10pt;
-margin-left: 2em;
-white-space: pre;
-}
-div.indent
-{ margin-left: 8%;
-margin-right: 0%;
-}
-.right { text-align: right; }
-.left { text-align: left; }
-.nowrap { white-space: nowrap; }
-.item_leader
-{ position: relative;
-margin-left: 8%;
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-.item_compact { position: absolute; vertical-align: baseline; }
-.item_cascade { position: relative; }
-.item_leftalign { text-align: left; }
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-{ width: 2em;
-text-align: right;
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-.item_compact .item_rightalign
-{ position: absolute;
-width: 52em;
-right: -2em;
-text-align: right;
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-{ position: relative;
-margin-left: 3em;
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-.smallcaps { font-size: smaller; text-transform: uppercase }
-/* END aephea.base.css */
-body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
-body
-{ text-align: justify;
-margin-left: 8%;
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-}
-</style>
-<title>The mcxdeblast manual</title>
-</head>
-<body>
-<p style="text-align:right">
-16 May 2014
-<a class="local" href="mcxdeblast.ps"><b>mcxdeblast</b></a>
-14-137
-</p>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#name">NAME</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#synopsis">SYNOPSIS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#description">DESCRIPTION</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#stream">STREAM MODE</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#assemble">ASSEMBLE MODE</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#options">OPTIONS</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#author">AUTHOR</a>
-</div>
-<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
-<div class=" item_text " style="margin-left:4em">
-<a class="intern" href="#sealso">SEE ALSO</a>
-</div>
-</div>
-
-<a name="name"></a>
-<h2>NAME</h2>
-<p style="margin-bottom:0" class="asd_par">
-mcxdeblast — parse BLAST files and stream
-output directly into mcl or write mcxassemble input.</p>
-
-<a name="synopsis"></a>
-<h2>SYNOPSIS</h2>
-<b>mcxdeblast</b> file-name
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdeblast</b>
-<a class="intern" href="#opt--score"><b>[--score=</b><b|e|r> (<i>bit scores|e-values|normalize bit score</i>)<b>]</b></a>
-<a class="intern" href="#opt--m9"><b>[--m9</b> (<i>expect BLAST column format</i>)<b>]</b></a>
-<a class="intern" href="#opt--out"><b>[--out</b> <fname> (<i>output file</i>)<b>]</b></a>
-<a class="intern" href="#opt--line-mode"><b>[--line-mode</b> abc (<i>write ID1 ID2 score format</i>)<b>]</b></a>
-<a class="intern" href="#opt--sort"><b>[--sort=</b><a|o> (<i>alphabetic|occurrence sorting</i>)<b>]</b></a>
-<a class="intern" href="#opt--xi-dat"><b>[--xi-dat=</b><suf> (<i>strip <suf> from file-name</i>)<b>]</b></a>
-<a class="intern" href="#opt--xo-dat"><b>[--xo-dat=</b><suf> (<i>add <suf> to base name</i>)<b>]</b></a>
-<a class="intern" href="#opt--bcut"><b>[--bcut=</b><val> (<i>bit score cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--ecut"><b>[--ecut=</b><val> (<i>E-value cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--rcut"><b>[--rcut=</b><val> (<i>raw value cutoff</i>)<b>]</b></a>
-<a class="intern" href="#opt--tab"><b>[--tab=</b><fname> (<i>tab file</i>)<b>]</b></a>
-<file-name></p>
-
-<a name="description"></a>
-<h2>DESCRIPTION</h2>
-<p style="margin-bottom:0" class="asd_par">
-<b>mcxdeblast</b> parses BLAST files.</p>
-<p style="margin-bottom:0" class="asd_par">
-In <i>stream mode</i> mcxdeblast output can be directly streamed to mcl by
-using the mcxdeblast <b>--line-mode</b>=<i>abc</i> option and equipping mcl with
-either <b>--abc</b> or <b>--expect-abc</b>. This can be considered the
-easy, lightweight and fast track. This functionality was recently acquired
-by mcl.</p>
-<p style="margin-bottom:0" class="asd_par">
-In the classic and slightly more heavy-handed <i>assemble mode</i>, mcxdeblast
-creates output files suitable for use by mcxassemble. The latter can in
-turn create input suitable for mcl. This is the mode in which mcxdeblast is
-employed by <b>mclblastline</b>.</p>
-
-<a name="stream"></a>
-<h2>STREAM MODE</h2>
-<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifiying <b>--line-mode</b>=<i>abc</i>.
-Use <b>--m9</b> if the input is in columnar output. Pipe the result
-to a file or directly to mcl. Example invocations can be found
-in <a class="local sibling" href="mcl.html">the mcl manual</a>.</p>
-
-<a name="assemble"></a>
-<h2>ASSEMBLE MODE</h2>
-<p style="margin-top:0em; margin-bottom:0em">
-If the input file is named <tt>iput</tt>, mcxdeblast will by
-default create files <tt>iput.hdr</tt>, <tt>iput.raw</tt>, <tt>iput.tab</tt>,
-<tt>iput.map</tt>, and <tt>iput.err</tt>. The <tt>hdr</tt> file contains
-information about the number of nodes found. It will be read
-by <a class="local sibling" href="mcxassemble.html">mcxassemble</a>. The <tt>raw</tt> file contains the co-occurrence
-scores between different nodes (peptides), also to be
-read by mcxassemble. The co-occurrence scores are in
-terms of mcl indentiers, which are subjected to rearranging
-by mcxassemble in order to correctly align them with the tab file.
-The <tt>tab</tt> file contains bindings between mcl identifiers
-(after rearranging as specified in the map file) and the BLAST labels
-(peptide identifiers). Refer to the manual of <a class="local sibling" href="mcxassemble.html">mcxassemble</a>
-for the syntax of a tab file.
-The <tt>err</tt> file contains a list of any errors encountered.</p>
-<p style="margin-bottom:0" class="asd_par">
-If the <b>--tab</b>=<b>fname</b> option is used mcxdeblast changes
-its behaviour. It will read the file <b>fname</b>, and use
-the bindings found therein. It will no longer output any
-of the <tt>hdr</tt>, <tt>map</tt>, or <tt>tab</tt> files. The <tt>hdr</tt>
-file should be provided by the same application that generated
-the specified tab file, and the <tt>map</tt> file should no longer be
-necessary (it might be convenient though and perhaps the
-future will bring a new <b>--map</b> option).</p>
-<p style="margin-bottom:0" class="asd_par">
-The <b>--tab</b>=<b>fname</b> option can be convenient e.g. if
-you split a BLAST job over multiple machines and want
-to apply mcxdeblast to each of the subresults. You do
-this by generating a single central tab file in advance.
-Then provide each instance of mcxdeblast with this tab file.
-Each instance will generate a <tt>raw</tt> file. The respective
-<tt>raw</tt> files can simply be concatenated and fed to mcxassemble
-using its <b>-raw</b> option. Additionally, a <tt>hdr</tt> file
-has to be specified for mcxassemble using its <b>-hdr</b>
-option. The syntax of <tt>hdr</tt> files is described in
-the <a class="local sibling" href="mcxassemble.html">mcxassemble</a> manual.
-Currently there is usually only one variable
-in the <tt>hdr</tt> file, which is the number of bindings
-listed in the tab file. This number, in turn, should equal
-the total number of different peptides encountered in the BLAST input.</p>
-
-<a name="options"></a>
-<h2>OPTIONS</h2>
-<div class=" itemize " style="margin-top:1em; font-size:100%">
-<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--tab"></a><b>--tab</b>=<fname> (<i>tab file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify a tab file to use, rather than automatically generating one.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--out"></a><b>--out</b> <fname> (<i>output file</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify the name for the output file.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--score"></a><b>--score</b>=<b|e|r> (<i>bit scores|e-values|norm bit score</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify whether to use bit scores, E-values, or bit scores
-normalized by length of the HSP.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--sort"></a><b>--sort</b>=<a|o> (<i>alphabetic|occurrence sorting</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Specify how to sort labels.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--m9"></a><b>--m9</b> (<i>expect BLAST column format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this option to parse BLAST output formatted with the -m 9 option.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--line-mode"></a><b>--line-mode</b>=abc (<i>write ID1 ID2 SCORE format</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Use this to stream output directly into mcl. Here <tt>abc</tt>
-is a literal; <b>--line-mode</b> may acquire other line output
-modes.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xi-dat"></a><b>--xi-dat</b>=<suf> (<i>strip <suf> from <file-name></i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-If set, the suffix <suf> is stripped from file-name in order
-to obtain the base name for output. If <file-name> does not
-end with suffix, it is assumed to be the base name, and <suf> is
-added in order to obtain the (real) file-name.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-dat"></a><b>--xo-dat</b>=<suf> (<i>add <suf> to base name</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Attaches the suffix to the base name. Use this to distinguish
-between different parses. One might for example
-use <b>--score</b>=<i>b</i> <b>--bcut</b>=<i>5</i> <b>--xo-dat</b>=<i>b</i>.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--bcut"></a><b>--bcut</b>=<val> (<i>bit score cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Bit scores below the cutoff value are ignored. This
-triggers the output of bit scores and ignores all other values.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ecut"></a><b>--ecut</b>=<val> (<i>E-value cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-E-values below the cutoff value are ignored. This triggers
-the output of E-values and ignores all other values.
-</p>
-</div>
-<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rcut"></a><b>--rcut</b>=<val> (<i>raw value cutoff</i>)</div></div>
-<div class=" item_text " style="margin-left:2em">
-<p style="margin-top:0em; margin-bottom:0em">
-Raw values below the cutoff value are ignored. This
-triggers the output of raw values and ignores all other values.
-</p>
-</div>
-</div>
-
-<a name="author"></a>
-<h2>AUTHOR</h2>
-Stijn van Dongen.
-Jason Stajich implemented the <b>--m9</b> option.
-Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments
-and fixes.
-
-<a name="sealso"></a>
-<h2>SEE ALSO</h2>
-<a class="local sibling" href="mclblastline.html">mclblastline</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>, <a class="local sibling" href="mcl.html">mcl</a>,
-<a class="local sibling" href="clmformat.html">clmformat</a>.
-</body>
-</html>
diff --git a/src/alien/oxygen/doc/mcxdeblast.ps b/src/alien/oxygen/doc/mcxdeblast.ps
deleted file mode 100644
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-# This Makefile.in is free software; the Free Software Foundation
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