[med-svn] r1123 - in trunk/packages/muscle/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Jan 12 07:15:14 UTC 2008
Author: charles-guest
Date: 2008-01-12 07:15:13 +0000 (Sat, 12 Jan 2008)
New Revision: 1123
Added:
trunk/packages/muscle/trunk/debian/muscle.html
trunk/packages/muscle/trunk/debian/patches/
trunk/packages/muscle/trunk/debian/patches/Makefile
Modified:
trunk/packages/muscle/trunk/debian/changelog
trunk/packages/muscle/trunk/debian/control
trunk/packages/muscle/trunk/debian/rules
Log:
swiching to quilt
Modified: trunk/packages/muscle/trunk/debian/changelog
===================================================================
--- trunk/packages/muscle/trunk/debian/changelog 2008-01-12 06:43:59 UTC (rev 1122)
+++ trunk/packages/muscle/trunk/debian/changelog 2008-01-12 07:15:13 UTC (rev 1123)
@@ -1,14 +1,17 @@
muscle (3.60-2) UNRELEASED; urgency=low
[ Charles Plessy ]
- * Add Subversion repository URL to debian/control.
- * Enhaces: seaview because SeaView can call muscle to re-align sequences.
+ * debian/control:
+ - Add Subversion repository.
+ - Swiched to quilt.
+ - Enhaces: seaview because SeaView can call muscle to re-align sequences.
+ - Moved the Homepage: field out from the package's description.
+ - Using debhelper 5.
+ - Removed [Biology] from package description as there are Debtags now.
+ - Checked that muscle conforms to Policy 3.7.3.
+ - Updated Steffen's email adress.
* Handling nostrip build option (policy 10.1) (Closes: #437599).
- * Updating Steffen's email adress.
* Updating manpage.
- * Using debhelper 5.
- * Removing [Biology] from package description as there are Debtags now.
- * Moved the Homepage: field out from the package's description.
[ Nelson A. de Oliveira ]
* Added watch file.
@@ -26,7 +29,7 @@
- manpages statically built
- minor changes
- -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 11:34:11 +0100
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 12 Jan 2008 15:48:55 +0900
muscle (3.60-1) unstable; urgency=low
Modified: trunk/packages/muscle/trunk/debian/control
===================================================================
--- trunk/packages/muscle/trunk/debian/control 2008-01-12 06:43:59 UTC (rev 1122)
+++ trunk/packages/muscle/trunk/debian/control 2008-01-12 07:15:13 UTC (rev 1123)
@@ -6,7 +6,7 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <charles-debian-nospam at plessy.org>,
David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5.0.0)
+Build-Depends: debhelper (>= 5.0.0), quilt
Standards-Version: 3.7.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle
Added: trunk/packages/muscle/trunk/debian/muscle.html
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.html (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.html 2008-01-12 07:15:13 UTC (rev 1123)
@@ -0,0 +1,2042 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 10 (filtered)">
+<title>MUSCLE User Guide</title>
+
+<style>
+<!--
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+</style>
+
+</head>
+
+<body lang=EN-US link=blue vlink=purple>
+
+<div class=Section1>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal align=right style='text-align:right'><span style='font-size:
+24.0pt;font-family:"Arial Black"'>MUSCLE User Guide</span></p>
+
+<p class=MsoNormal align=right style='text-align:right'><u> </u></p>
+
+<p class=MsoNormal align=right style='text-align:right'><b><span
+style='font-family:Arial'> </span></b></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>Multiple sequence comparison
+by log-expectation</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>by Robert C. Edgar</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>Version 3.5</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>August 2004</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'><a
+href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a></span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>email: muscle (at) drive5.com</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>MUSCLE is updated regularly.
+Send me an e-mail if you would like to be notified of new releases.</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><i><span style='font-family:Arial'>Citation:</span></i></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'><a
+href="http://nar.oupjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&keytype=ref">Edgar,
+Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and
+high throughput, <i>Nucleic Acids Research</i> <b>32</b>(5), 1792-97</a>.</span></p>
+
+<span style='font-size:10.0pt;font-family:Arial'><br clear=all
+style='page-break-before:always'>
+</span>
+
+<p class=MsoNormal><b><span style='font-size:16.0pt;font-family:Arial'>Table of
+Contents</span></b></p>
+
+<p class=MsoToc1><span
+class=MsoHyperlink><a href="#_Toc81224823">1 Introduction<span
+style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224824">2 Quick Start<span
+style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224825">2.1
+Installation<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224826">2.2 Making an
+alignment<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224827">2.3 Large
+alignments<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224828">2.4 Fastest
+speed<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224829">2.5 Huge
+alignments<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224830">2.6 Accuracy:
+caveat emptor<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224831">2.7
+Pipelining<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224832">2.8 Refining
+an existing alignment<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224833">2.9
+Profile-profile alignment<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224834">2.10 Sequence
+clustering<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224835">3 File
+Formats<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224836">3.1 Input
+files<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224837">3.1.1 Amino
+acid sequences<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224838">3.1.2
+Nucleotide sequences<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224839">3.1.3
+Determining sequence type<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224840">3.2 Output
+files<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224841">3.2.1
+Sequence grouping<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224842">3.3 CLUSTALW
+format<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224843">3.4 MSF format<span
+style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224844">3.5 HTML
+format<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224845">4 Using
+MUSCLE<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224846">4.1 How the
+algorithm works<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224847">4.2
+Command-line options<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>7</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224848">4.3 The
+maxiters option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>7</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224849">4.4 The
+maxtrees option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224850">4.5 The
+maxhours option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224851">4.6 The
+profile scoring function<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224852">4.7 Diagonal
+optimization<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224853">4.8 Anchor
+optimization<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224854">4.9 Log file<span
+style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224855">4.10 Progress
+messages<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224856">4.11 Running
+out of memory<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224857">4.12
+Troubleshooting<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224858">4.13
+Technical support<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>10</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224859">5 Command
+Line Reference<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>10</span></a></span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<b><span style='font-size:16.0pt;font-family:Arial'><br clear=all
+style='page-break-before:always'>
+</span></b>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224823">1 Introduction</a></h1>
+
+<p class=MsoNormal>MUSCLE is a program for creating multiple alignments of
+amino acid or nucleotide sequences. A range of options is provided that give
+you the choice of optimizing accuracy, speed, or some compromise between the
+two. Default parameters are those that give the best average accuracy in our
+tests. Using versions current at the time of writing, my tests show that MUSCLE
+can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee,
+depending on the chosen options.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224824">2 Quick
+Start</a></h1>
+
+<p class=MsoNormal>The MUSCLE algorithm is delivered as a command-line program
+called <i>muscle</i>. If you are running under Linux or Unix you will be
+working at a shell prompt. If you are running under Windows, you should be in a
+command window (nostalgically known to us older people as a DOS prompt). If you
+don't know how to use command-line programs, you should get help from a local
+guru.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224825">2.1 Installation</a></h2>
+
+<p class=MsoNormal>Copy the <i>muscle</i> binary file to a directory that is
+accessible from your computer. That's it—there are no configuration files,
+libraries, environment variables or other settings to worry about. If you are
+using Windows, then the binary file is named <i>muscle.exe</i>. From now on <i>muscle</i>
+should be understood to mean "<i>muscle</i> if you are using Linux or Unix,
+<i>muscle.exe</i> if you are using Windows".</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224826">2.2 Making an
+alignment</a></h2>
+
+<p class=MsoNormal>Make a FASTA file containing some sequences. (If you are not
+familiar with FASTA format, it is described in detail later in this Guide.) For
+now, just to make things fast, limit the number of sequence in the file to no
+more than 50 and the sequence length to be no more than 500. Call the input
+file <i>seqs.fa</i>. (An example file named <i>seqs.fa</i> is distributed with
+the standard MUSCLE package). Make sure the directory containing the <i>muscle</i>
+binary is in your path. (If it isn't, you can run it by typing the full path
+name, and the following example command lines must be changed accordingly). Now
+type:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>You should see some progress messages. If <i>muscle</i>
+completes successfully, it will create a file <i>seqs.afa</i> containing the
+alignment. By default, output is created in "aligned FASTA" format
+(hence the <i>.afa</i> extension). This is just like regular FASTA except that
+gaps are added in order to align the sequences. This is a nice format for
+computers but not very readable for people, so to look at the alignment you
+will want an alignment viewer such as Belvu, or a script that converts FASTA to
+a more readable format. You can also use the –<i>msf</i> command-line option to
+request output in MSF format, which is easier to understand for people. If <i>muscle</i>
+gives an error message and you don't know how to fix it, please read the
+Troubleshooting section.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The default settings are designed to give the best accuracy,
+so this may be all you need to know.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224827">2.3 Large
+alignments</a></h2>
+
+<p class=MsoNormal>If you have a large number of sequences (a few thousand), or
+they are very long, then the default settings of may be too slow for practical
+use. A good compromise between speed and accuracy is to run just the first two
+iterations of the algorithm. On average, this gives accuracy equal to T-Coffee
+and speeds much faster than CLUSTALW. This is done by the option <i>–maxiters 2</i>,
+as in the following example.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 2</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224828">2.4 Fastest
+speed</a></h2>
+
+<p class=MsoNormal>If you want the fastest possible speed, then the following
+example shows the applicable options for proteins.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv -distance1
+kbit20_3</p>
+
+<p class=Code> </p>
+
+<p class=MsoNormal>For nucleotides, use:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>At the time of writing, <i>muscle</i> with these options is faster
+than any other multiple sequence alignment program that I have tested. The
+alignments are not bad, especially when the sequences are closely related.
+However, as you might expect, this blazing speed comes at the cost of the
+lowest average accuracy of the options that <i>muscle</i> provides.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224829">2.5 Huge
+alignments</a></h2>
+
+<p class=MsoNormal>If you have a <i>very</i> large number of sequences (several
+thousand), or they are very long, then the <i>kbit20_3</i> option may cause
+problems because it needs a relatively large amount of memory. Better is to use
+the default distance measure, which is roughly 2× or 3× slower but needs less
+memory, like this:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224830">2.6 Accuracy:
+caveat emptor</a></h2>
+
+<p class=MsoNormal>Why do I keep using the clumsy phrase "average
+accuracy" instead of just saying "accuracy"? That's because the
+quality of alignments produced by MUSCLE varies, as do those produced other programs
+such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for
+improvement. Sometimes the fastest speed options to <i>muscle</i> give
+alignments that are better than T-Coffee, though the reverse will more often be
+the case. With challenging sets of sequences, it is a good idea to make several
+different alignments using different <i>muscle</i> options and to try other programs
+too. Regions where different alignments agree are more believable than regions
+where they disagree. </p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224831">2.7 Pipelining</a></h2>
+
+<p class=MsoNormal>Input can be taken from standard input, and output can be
+written to standard output. This is the default, so our first example would
+also work like this:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle < seqs.fa > seqs.afa</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224832">2.8 Refining
+an existing alignment</a></h2>
+
+<p class=MsoNormal>You can ask <i>muscle</i> to try to improve an existing alignment
+by using the –<i>refine</i> option. The input file must then be a FASTA file
+containing an alignment. All sequences must be of equal length, gaps can be
+specified using dots "." or dashes "–". For example:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in seqs.afa -out refined.afa -refine</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224833">2.9 Profile-profile
+alignment</a></h2>
+
+<p class=MsoNormal>A fundamental step in the MUSCLE algorithm is aligning two
+multiple sequence alignments, each of which contain some of the input
+sequences. This operation is sometimes called "profile-profile
+alignment". If you have two existing alignments of related sequences you
+can use the <i>–profile</i> option of MUSCLE to align those two sequences.
+Typical usage is:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -profile -in1 one.afa -in2 two.afa -out both.afa</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The alignments in <i>one.afa</i> and <i>two.afa</i>, which
+must be in aligned FASTA format, are aligned to each other, keeping input
+columns intact and inserting columns of gaps where needed. Output is stored in <i>both.afa</i>.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>MUSCLE does not compute a similarity measure or measure of
+statistical significance (such as an E-value), so this option is not useful for
+discriminating homologs from unrelated sequences. For this task, I recommend Sadreyev
+& Grishin's COMPASS program.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224834">2.10 Sequence
+clustering</a></h2>
+
+<p class=MsoNormal>The first stage in MUSCLE is a fast clustering algorithm.
+This may be of use in other applications. Typical usage is:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -cluster -in seqs.fa -tree1 tree.phy</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The sequences will be clustered, and a tree written to <i>tree.phy</i>.
+Options –<i>weight1</i>, –<i>distance1</i>, –<i>cluster1</i> and –<i>root1</i> can
+be applied if desired. Note that by default, UPGMA clustering is used. You can
+use</p>
+
+<p class=MsoNormal> –<i>neighborjoining</i> if you prefer, but note that this
+is substantially slower than UPGMA for large numbers of sequences.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224835">3 File
+Formats</a></h1>
+
+<p class=MsoNormal>MUSCLE uses FASTA format for both input and output. For
+output only, it also offers CLUSTALW, MSF and HTML formats using the –<i>clw</i>,
+–<i>msf</i> and –<i>html</i> command-line options.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224836">3.1 Input
+files</a></h2>
+
+<p class=MsoNormal>Input files must be in FASTA format. These are plain text
+files (word processing files such as Word documents are not understood!). Unix,
+Windows and DOS text files are supported (end-of-line may be NL or CR NL). There
+is no explicit limit on the length of a sequence, however if you are running a
+32-bit version of <i>muscle</i> then the maximum will be very roughly 10,000 letters
+due to maximum addressable size of tables required in memory. Each sequence starts
+with an annotation line, which is recognized by having a greater-than symbol
+">" as its first character. There is no limit on the length of an
+annotation line (this is new as of version 3.5), and there is no requirement
+that the annotation be unique. The sequence itself follows on one or more
+subsequent lines, and is terminated either by the next annotation line or by
+the end of the file. </p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224837">3.1.1 Amino
+acid sequences</a></h3>
+
+<p class=MsoNormal>The standard single-letter amino acid alphabet is used. Upper
+and lower case is allowed, the case is not significant. The special characters
+X, B, Z and U are understood. X means "unknown amino acid", B is D or
+N, Z is E or Q. U is understood to be the 21st amino acid Selenocysteine. White
+space (spaces, tabs and the end-of-line characters CR and NL) is allowed inside
+sequence data. Dots "." and dashes "–" in sequences are
+allowed and are discarded unless the input is expected to be aligned (e.g. for
+the –<i>refine</i> option). </p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224838">3.1.2 Nucleotide
+sequences</a></h3>
+
+<p class=MsoNormal>The usual letters A, G, C, T and U stand for nucleotides.
+The letters T and U are equivalent as far as MUSCLE is concerned. N is the
+wildcard meaning "unknown nucleotide". R means A or G, Y means C or
+T/U. Other wildcards, such as those used by RFAM, are not understood in this
+version and will be replaced by Ns. If you would like support for other DNA /
+RNA alphabets, please let me know.</p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224839">3.1.3 Determining
+sequence type</a></h3>
+
+<p class=MsoNormal>By default, MUSCLE looks at the first 100 letters in the
+input sequence data (excluding gaps). If 95% or more of those letters are valid
+nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as
+amino acids. This method almost always guesses correctly, but you can make sure
+by specifying the sequence type on the command line. This is done using the –<i>seqtype</i>
+option, which can take the following values:</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal> –<i>seqtype protein</i> Amino
+acid</p>
+
+<p class=MsoNormal> –s<i>eqtype nucleo</i> Nucleotide</p>
+
+<p class=MsoNormal> –<i>seqtype auto</i> Automatic
+detection (default).</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224840">3.2 Output
+files</a></h2>
+
+<p class=MsoNormal>By default, output is also written in FASTA format. All
+letters are upper-case and gaps are represented by dashes "–".</p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224841">3.2.1 Sequence
+grouping</a></h3>
+
+<p class=MsoNormal>By default, MUSCLE re-arranges sequences so that similar
+sequences are adjacent in the output file. (This is done by ordering sequences
+according to a prefix traversal of the guide tree). This makes the alignment
+easier to evaluate by eye. If you want to the sequences to be output in the
+same order as the input file, you can use the –<i>stable</i> option.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224842">3.3 CLUSTALW
+format</a></h2>
+
+<p class=MsoNormal>You can request CLUSTALW output by using the –<i>clw</i>
+option. This should be compatible with CLUSTALW, with the exception of the
+program name in the file header. You can ask MUSCLE to impersonate CLUSTALW by
+writing "CLUSTAL W (1.81)" as the program name by using –<i>clwstrict</i>.
+If you have problems parsing MUSCLE output with scripts designed for CLUSTALW,
+please let me know.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224843">3.4 MSF format</a></h2>
+
+<p class=MsoNormal>MSF format (similar to CLUSTALW) is requested by using the –<i>msf</i>
+option. As with CLUSTALW format, this is easier for people to read than FASTA.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224844">3.5 HTML
+format</a></h2>
+
+<p class=MsoNormal>I've added an experimental feature starting in version 3.4. To
+get a Web page as output, use the –<i>html</i> option. The alignment is colored
+using a color scheme from Eric Sonnhammer's Belvu editor, which is my personal
+favorite. A drawback of this option is that the Web page typically contains a
+very large number of HTML tags, which can be slow to display in the Internet
+Explorer browser. The Netscape browser works much better. If you have any ideas
+about good ways to make Web pages, please let me know.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224845">4 Using
+MUSCLE</a></h1>
+
+<p class=MsoNormal>In this section we give more details of the MUSCLE algorithm
+and the more important options offered by the <i>muscle</i> implementation.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224846">4.1 How the
+algorithm works</a></h2>
+
+<p class=MsoNormal>We won't give a complete description of the MUSCLE algorithm
+here—for that, you will have to read the paper. But hopefully a summary will
+help explain what some of the command-line options do and how they might be
+useful in your work.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The first step is to calculate a tree. In CLUSTALW, this is
+done as follows. Each pair of input sequences is aligned, and used to compute
+the pair-wise identity of the pair. Identities are converted to a measure of
+distance. Finally, the distance matrix is converted to a tree using a
+clustering method (CLUSTALW uses neighbor-joining). If you have 1,000
+sequences, there are (1,000 <span style='font-family:Symbol'>´</span> 999)/2 =
+499,500 pairs, so aligning every pair can take a while. MUSCLE uses a much
+faster, but somewhat more approximate, method to compute distances: it counts
+the number of short sub-sequences (known as <i>k</i>-mers, <i>k</i>-tuples or
+words) that two sequences have in common, without constructing an alignment.
+This is typically around 3,000 times faster that CLUSTALW's method, but the trees
+will generally be less accurate. We call this step "<i>k</i>-mer
+clustering".</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The second step is to use the tree to construct what is
+known as a progressive alignment. At each node of the binary tree, a pair-wise
+alignment is constructed, progressing from the leaves towards the root. The
+first alignment will be made from two sequences. Later alignments will be one
+of the three following types: sequence-sequence, profile-sequence or
+profile-profile, where "profile" means the multiple alignment of the sequences
+under a given internal node of the tree. This is very similar to what CLUSTALW
+does once it has built a tree.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>Now we have a multiple
+alignment, which has been built very quickly compared with conventional methods,
+mainly because of the distance calculation using <i>k</i>-mers rather than
+alignments. The quality of this alignment is typically pretty good—it will
+often tie or beat a T-Coffee alignment on our tests. However, on average, we
+find that it can be improved by proceeding through the following steps.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>From the multiple alignment,
+we can now compute the pair-wise identities of each pair of sequences. This
+gives us a new distance matrix, from which we estimate a new tree. We compare
+the old and new trees, and re-align subgroups where needed to produce a
+progressive multiple alignment from the new tree. If the two trees are
+identical, there is nothing to do; if there are no subtrees that agree (very unusual),
+then the whole progressive alignment procedure must be repeated from scratch.
+Typically we find that the tree is pretty stable near the leaves, but some
+re-alignments are needed closer the root. This procedure (compute pair-wise
+identities, estimate new tree, compare trees, re-align) is iterated until the
+tree stabilizes or until a specified maximum number of iterations has been
+done. We call this process "tree refinement", although it also tends
+to improve the alignment.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>We now keep the tree fixed
+and move to a new procedure which is designed to improve the multiple
+alignment. The set of sequences is divided into two subsets (i.e., we make a
+bipartition on the set of sequences). A profile is constructed for each of the
+two subsets based on the current multiple alignment. These two profiles are
+then re-aligned to each other using the same pair-wise alignment algorithm as
+used in the progressive stage. If this improves an "objective score"
+that measures the quality of the alignment, then the new multiple alignment is
+kept, otherwise it is discarded. By default, the objective score is the classic
+sum-of-pairs score that takes the (sequence weighted) average of the pair-wise
+alignment score of every pair of sequences in the alignment. Bipartitions are
+chosen by deleting an edge in the guide tree, each of the two resulting
+subtrees defines a subset of sequences. This procedure is called "tree
+dependent refinement". One iteration of tree dependent refinement tries
+bipartitions produced by deleting every edge of the tree in depth order moving
+from the leaves towards the center of the tree. Iterations continue until
+convergence or up to a specified maximum.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>For convenience, the major
+steps in MUSCLE are described as "iterations", though the first three
+iterations all do quite different things and may take very different lengths of
+time to complete. The tree-dependent refinement iterations 3, 4 ... are true
+iterations and will take similar lengths of time. </p>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <tr>
+ <td width=89 valign=top style='width:66.6pt;border:none;border-bottom:solid windowtext 1.0pt;
+ padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Iteration</span></b></p>
+ </td>
+ <td width=461 valign=top style='width:4.8in;border:none;border-bottom:solid windowtext 1.0pt;
+ padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Actions</span></b></p>
+ </td>
+ </tr>
+ <tr>
+ <td width=89 valign=top style='width:66.6pt;border:none;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>1</p>
+ </td>
+ <td width=461 valign=top style='width:4.8in;border:none;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by <i>k</i>-mer
+ clustering, estimate tree, progressive alignment according to this tree.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>2</p>
+ </td>
+ <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by
+ pair-wise identities from current multiple alignment, estimate tree,
+ progressive alignment according to new tree, repeat until convergence or specified
+ maximum number of times.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>3, 4 ...</p>
+ </td>
+ <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Tree-dependent refinement. One
+ iteration visits every edge in the tree one time.</p>
+ </td>
+ </tr>
+</table>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224847">4.2 Command-line
+options</a></h2>
+
+<p class=MsoNormal>There are two types of command-line options: value options
+and flag options. Value options are followed by the value of the given
+parameter, for example –<i>in <filename></i>; flag options just stand for
+themselves, such as –<i>msf</i>. All options are a dash (not two dashes!)
+followed by a long name; there are no single-letter equivalents. Value options
+must be separated from their values by white space in the command line. Thus, <i>muscle</i>
+does not follow Unix, Linux or Posix standards, for which we apologize. The
+order in which options are given is irrelevant unless two options contradict,
+in which case the right-most option silently wins.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224848">4.3 The
+maxiters option</a></h2>
+
+<p class=MsoNormal>You can control the number of iterations that MUSCLE does by
+specifying the <i>–maxiters</i> option. If you specify 1, 2 or 3, then this is
+exactly the number of iterations that will be performed. If the value is
+greater than 3, then <i>muscle</i> will continue up to the maximum you specify
+or until convergence is reached, which ever happens sooner. The default is 16.
+If you have a large number of sequences, refinement may be rather slow.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224849">4.4 The maxtrees
+option</a></h2>
+
+<p class=MsoNormal>This option controls the maximum number of new trees to
+create in iteration 2. Our experience suggests that a point of diminishing
+returns is typically reached after the first tree, so the default value is 1.
+If a larger value is given, the process will repeat until convergence or until
+this number of trees has been created, which ever comes first.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224850">4.5 The maxhours
+option</a></h2>
+
+<p class=MsoNormal>If you have a large alignment, <i>muscle</i> may take a long
+time to complete. It is sometimes convenient to say "I want the best
+alignment I can get in 24 hours" rather than specifying a set of options
+that will take an unknown length of time. This is done by using <i>–maxhours</i>,
+which specifies a floating-point number of hours. If this time is exceeded, <i>muscle</i>
+will write out current alignment and stop. For example,</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>Note that the actual time may exceed the specified limit by
+a few minutes while <i>muscle</i> finishes up on a step. It is also possible
+for no alignment to be produced if the time limit is too small.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224851">4.6 The
+profile scoring function</a></h2>
+
+<p class=MsoNormal>Three different protein profile scoring functions are
+supported, the log-expectation score (–<i>le</i> option) and a sum of pairs
+score using either the PAM200 matrix (–<i>sp</i>) or the VTML240 matrix (–<i>sv</i>).
+The log-expectation score is the default as it gives better results on our
+tests, but is typically somewhere between two or three times slower than the
+sum-of-pairs score. For nucleotides, –<i>spn</i> is currently the only option
+(which is of course the default for nucleotide data, so you don't need to
+specify this option).</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224852">4.7 Diagonal
+optimization</a></h2>
+
+<p class=MsoNormal>Creating a pair-wise alignment by dynamic programming
+requires computing an <i>L</i><sub>1</sub> <span style='font-family:Symbol'>´</span>
+<i>L</i><sub>2</sub> matrix, where <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub>
+are the sequence lengths. A trick used in algorithms such as BLAST is to reduce
+the size of this matrix by using fast methods to find "diagonals",
+i.e. short regions of high similarity between the two sequences. This speeds up
+the algorithm at the expense of some reduction in accuracy. MUSCLE uses a
+technique called <i>k</i>-mer extension to find diagonals. It is disabled by
+default because of the slight reduction in average accuracy and can be turned
+on by specifying the –<i>diags1</i> and <i>–diags2</i> options.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224853">4.8 Anchor
+optimization</a></h2>
+
+<p class=MsoNormal>Tree-dependent refinement (iterations 3, 4 ... ) can be
+speeded up by dividing the alignment vertically into blocks. Block boundaries
+are found by identifying high-scoring columns (e.g., a perfectly conserved
+column of Cs or Ws would be a candidate). Each vertical block is then refined
+independently before reassembling the complete alignment, which is faster
+because of the <i>L</i><sup>2</sup> factor in dynamic programming (e.g.,
+suppose the alignment is split into two vertical blocks, then 2 <span
+style='font-family:Symbol'>´</span> 0.5<sup>2</sup> = 0.5, so the dynamic
+programming time is roughly halved). The –<i>noanchors</i> option is used to disable
+this feature. This option has no effect if <i>–maxiters 1</i> or –<i>maxiters 2</i>
+is specified. On benchmark tests, enabling anchors has little or no effect on
+accuracy, but if you want to be very conservative and are striving for the best
+possible accuracy then –<i>noanchors</i> is a reasonable choice.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224854">4.9 Log file</a></h2>
+
+<p class=MsoNormal>You can specify a log file by using –<i>log <filename></i>
+or –<i>loga <filename></i>. Using –<i>log</i> causes any existing file to
+be deleted, –<i>loga</i> appends to any existing file. A message will be
+written to the log file when <i>muscle</i> starts and stops. Error and warning
+messages will also be written to the log. If –<i>verbose</i> is specified, then
+more information will be written, including the command line used to invoke <i>muscle</i>,
+the resulting internal parameter settings, and also progress messages. The
+content and format of verbose log file output is subject to change in future
+versions. </p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The use of a log file may seem contrary to Unix conventions for
+using standard output and standard error. I like these conventions, but never
+found a fully satisfactory way to use them. I like progress messages (see
+below), but they mess up a file if you re-direct standard error and there are
+errors or warning messages too. I could try to detect whether a standard file
+handle is a <i>tty</i> device or a disk file and change behavior accordingly,
+but I regard this as too complicated and too hard for the user to understand. On
+Windows it can be hard to re-direct standard file handles, especially when
+working in a GUI debugger. Maybe one day I will figure out a better solution
+(suggestions welcomed).</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>I highly recommend using –<i>verbose </i>and –<i>log[a]</i>,
+especially when running <i>muscle</i> in a batch mode. This enables you to
+verify whether a particular alignment was completed and to review any errors or
+warnings that occurred.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224855">4.10 Progress
+messages</a></h2>
+
+<p class=MsoNormal>By default, <i>muscle</i> writes progress messages to
+standard error periodically so that you know it's doing something and get some
+feedback about the time and memory requirements for the alignment. Here is a
+typical progress message.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=Code>00:00:23 25 Mb Iter 2 87.20% Build guide tree</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>The fields are as follows.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <tr>
+ <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=Code style='page-break-after:avoid'>00:00:23</p>
+ </td>
+ <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Elapsed time since <i>muscle</i>
+ started.</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=Code style='page-break-after:avoid'>25 Mb</p>
+ </td>
+ <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Peak memory use in megabytes
+ (i.e., not the current usage, but the maximum amount of memory used since <i>muscle</i>
+ started).</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=Code style='page-break-after:avoid'>Iter 2</p>
+ </td>
+ <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Iteration currently in
+ progress.</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=Code style='page-break-after:avoid'>87.20%</p>
+ </td>
+ <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>How much of the current step
+ has been completed (percentage).</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=Code>Build...</p>
+ </td>
+ <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>A brief description of the current step.</p>
+ </td>
+ </tr>
+</table>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>The –<i>quiet</i> command-line option disables writing
+progress messages to standard error. If the –<i>verbose</i> command-line option
+is specified, a progress message will be written to the log file when each
+iteration completes. So –<i>quiet</i> and –<i>verbose</i> are not
+contradictory.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224856">4.11 Running
+out of memory</a></h2>
+
+<p class=MsoNormal>The <i>muscle</i> code tries to deal gracefully with
+low-memory conditions by using the following technique. A block of "emergency
+reserve" memory is allocated when <i>muscle</i> starts. If a later request
+to allocate memory fails, this reserve block is made available, and <i>muscle</i>
+attempts to save the current alignment. With luck, the reserved memory will be
+enough to allow <i>muscle</i> to save the alignment and exit gracefully with an
+informative error message.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224857">4.12 Troubleshooting</a></h2>
+
+<p class=MsoNormal>Here is some general advice on what to do if <i>muscle</i>
+fails and you don't understand what happened. The code is designed to fail
+gracefully with an informative error message when something goes wrong, but
+there will no doubt be situations I haven't anticipated (not to mention bugs).</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>Check the MUSCLE web site for updates, bug reports and other
+relevant information.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal style='page-break-after:avoid'> <a
+href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a></p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>Check the input file to make sure it is in valid FASTA format.
+Try giving it to another sequence analysis program that can accept large FASTA
+files (e.g., the NCBI <i>formatdb</i> utility) to see if you get an informative
+error message. Try dividing the file into two halves and using each half
+individually as input. If one half fails and the other does not, repeat until
+the problem is localized as far as possible.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>Use –<i>log</i> or –<i>loga</i> and –<i>verbose</i> and
+check the log file to see if there are any messages that give you a hint about the
+problem. Look at the peak memory requirements (reported in progress messages)
+to see if you may be exceeding the physical or virtual memory capacity of your
+computer.</p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal>If <i>muscle</i> crashes without giving an error message, or
+hangs, then you may need to refer to the source code or use a debugger. A
+"debug" version, <i>muscled</i>, may be provided. This is built from
+the same source code but with the DEBUG macro defined and without compiler
+optimizations. This version runs much more slowly (perhaps by a factor of three
+or more), but does a lot more internal checking and may be able to catch
+something that is going wrong in the code. The –<i>core</i> option specifies
+that <i>muscle</i> should not catch exceptions. When –<i>core</i> is specified,
+an exception may result in a debugger trap or a core dump, depending on the
+execution environment. The –<i>nocore</i> option has the opposite effect. In <i>muscle</i>,
+–<i>nocore</i> is the default, –<i>core</i> is the default in <i>muscled</i>.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224858">4.13 Technical
+support</a></h2>
+
+<p class=MsoNormal>I am happy to provide support. But I am busy, and am
+offering this program at no charge, so I ask you to make a reasonable effort to
+figure things out for yourself before contacting me.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224859">5 Command Line
+Reference</a></h1>
+
+<p class=MsoNormal style='page-break-after:avoid'> </p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <thead>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;border:none;border-bottom:
+ solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Value option</span></b></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;border:none;border-bottom:solid windowtext 1.0pt;
+ padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Legal values</span></b></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;border:none;border-bottom:
+ solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Default</span></b></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;border:none;border-bottom:
+ solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Description</span></b></p>
+ </td>
+ </tr>
+ </thead>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>anchorspacing</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>32</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Minimum spacing between
+ anchor columns.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>center</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Center parameter. Should be
+ negative.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>cluster1</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>cluster2</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>upgma</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>upgmb</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>neighborjoining</span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>upgmb</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Clustering method. cluster1
+ is used in iteration 1 and 2, cluster2 in later iterations.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>diaglength</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>24</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Minimum length of diagonal.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>diagmargin</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>5</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Discard this many positions
+ at ends of diagonal.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance1</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'> </span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer4_6</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'> </span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Kmer6_6
+ (amino) or Kmer4_6 (nucleo)</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Distance measure for iteration 1.</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance2</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'> </span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_kimura</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_log</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'> </span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_kimura</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Distance measure for iterations 2, 3 ...</p>
+ <p class=MsoNormal> </p>
+ <p class=MsoNormal> </p>
+ <p class=MsoNormal> </p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>gapopen</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>[1]</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>The gap open score. Must be negative.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydro</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>5</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Window size for determining whether a region is
+ hydrophobic.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydrofactor</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1.2</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Multiplier for gap open/close penalties in hydrophobic
+ regions.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Any file name</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>standard input</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Where to find the input sequences.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>log</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>File name</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>None.</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Log file name (delete existing file).</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>loga</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>File name</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>None.</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Log file name (append to existing file).</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxdiagbreak</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>1</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Maximum distance between two diagonals that allows them to
+ merge into one diagonal.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxhours</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>None.</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Maximum time to run in hours. The actual time may exceed
+ the requested limit by a few minutes. Decimals are allowed, so 1.5 means one
+ hour and 30 minutes.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxiters</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Integer 1, 2 ...</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>16</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Maximum number of iterations.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxtrees</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Maximum number of new trees to build in iteration 2.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>minbestcolscore</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Floating point </p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Minimum score a column must
+ have to be an anchor.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>minsmoothscore</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Minimum smoothed score a
+ column must have to be an anchor.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>objscore</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sp</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>ps</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>dp</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>xp</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spf</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spm</span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spm</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Objective score used by tree dependent refinement.</p>
+ <p class=MsoNormal>sp=sum-of-pairs score.</p>
+ <p class=MsoNormal>spf=sum-of-pairs score (dimer approximation)</p>
+ <p class=MsoNormal>spm=sp for < 100 seqs, otherwise spf</p>
+ <p class=MsoNormal>dp=dynamic programming score.</p>
+ <p class=MsoNormal>ps=average profile-sequence score.</p>
+ <p class=MsoNormal>xp=cross profile score.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>out</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>File name</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>standard output</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Where to write the alignment.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root1</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root2</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pseudo</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>midlongestspan</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>minavgleafdist</span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>psuedo</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Method used to root tree; root1 is used in iteration 1 and
+ 2, root2 in later iterations.</p>
+ <p class=MsoNormal> </p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>seqtype</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>protein</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>nucleo</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'> </span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Sequence type.</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>smoothscoreceil</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Floating point</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>[1]</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Maximum value of column score for smoothing purposes.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>smoothwindow</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Integer</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>7</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Window used for anchor column smoothing.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>SUEFF</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Floating point value between 0 and 1.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>0.1</span></p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Constant used in UPGMB clustering. Determines the relative
+ fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1 – SUEFF).<br>
+ <br>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree1</span></p>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree2</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>File name</p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>None</p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Save tree produced in first or second iteration to given
+ file in Newick (Phylip-compatible) format.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>weight1</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>weight2</span></p>
+ </td>
+ <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>none</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>henikoff</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>henikoffpb</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>gsc</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>clustalw</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>threeway</span></p>
+ </td>
+ <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>clustalw</span></p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Sequence weighting scheme.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>weight1 is used in
+ iterations 1 and 2.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>weight2 is used for
+ tree-dependent refinement.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>none=all sequences have
+ equal weight.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>henikoff=Henikoff &
+ Henikoff weighting scheme.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>henikoffpb=Modified
+ Henikoff scheme as used in PSI-BLAST.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>clustalw=CLUSTALW method.</p>
+ <p class=MsoNormal style='page-break-after:avoid'>threeway=Gotoh three-way
+ method.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+</table>
+
+<p class=MsoNormal> </p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <thead>
+ <tr>
+ <td width=137 valign=top style='width:102.6pt;border:none;border-bottom:
+ solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Flag option</span></b></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;border:none;border-bottom:solid windowtext 1.0pt;
+ padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Set by default?</span></b></p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;border:none;border-bottom:
+ solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+ 9.0pt;font-family:Arial'>Description</span></b></p>
+ </td>
+ </tr>
+ </thead>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>anchors</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Use anchor optimization in
+ tree dependent refinement iterations.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>clw</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
+ format (default is FASTA).</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>clwstrict</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
+ format with the "CLUSTAL W (1.81)" header rather than the MUSCLE
+ version. This is useful when a post-processing step is picky about the file
+ header.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>core</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>yes in muscle,</p>
+ <p class=MsoNormal style='page-break-after:avoid'>no in muscled.</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Do not catch exceptions.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>fasta</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Write output in FASTA
+ format. Alternatives include –<i>clw</i>,</p>
+ <p class=MsoNormal style='page-break-after:avoid'>–<i>clwstrict, –msf</i> and
+ –<i>html</i>.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>group</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Group similar sequences
+ together in the output. This is the default. See also –<i>stable</i>.</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>html</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'>Write output in HTML format
+ (default is FASTA).</p>
+ <p class=MsoNormal style='page-break-after:avoid'> </p>
+ </td>
+ </tr>
+ <tr>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>le</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>maybe</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt'>
+ <p class=MsoNormal>Use log-expectation profile score (VTML240). Alternatives
+ are to use –<i>sp</i> or <i>–sv</i>. This is the default for amino acid
+ sequences.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>msf</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Write output in MSF format (default is FASTA).</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>noanchors</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Disable anchor optimization. Default is –<i>anchors</i>.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>nocore</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no in muscle,</p>
+ <p class=MsoNormal>yes in muscled.</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Catch exceptions and give an error message if possible.</p>
+ <p class=MsoNormal> </p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>quiet</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Do not display progress messages.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>refine</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Input file is already aligned, skip first two iterations
+ and begin tree dependent refinement.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>sp</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Use sum-of-pairs protein profile score (PAM200). Default
+ is –<i>le.</i></p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>spn</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>maybe</p>
+ <p class=MsoNormal> </p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Use sum-of-pairs nucleotide profile score (BLASTZ
+ parameters). This is the only option for nucleotides, and is therefore the
+ default.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+ 8.0pt;font-family:"Courier New"'>stable</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Preserve input order of sequences in output file. Default
+ is to group sequences by similarity (–<i>group</i>).</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sv</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Use sum-of-pairs profile score (VTML240). Default is –<i>le.</i></p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapsfull</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Terminal gaps penalized with full penalty.</p>
+ <p class=MsoNormal>[1] Not fully supported in this version.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapshalf</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>yes</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Terminal gaps penalized with half penalty.</p>
+ <p class=MsoNormal>[1] Not fully supported in this version.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapshalflonger</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Terminal gaps penalized with half penalty if gap relative
+ to </p>
+ <p class=MsoNormal>longer sequence, otherwise with full penalty.</p>
+ <p class=MsoNormal>[1] Not fully supported in this version.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>verbose</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Write parameter settings and progress messages to log
+ file.</p>
+ <p class=MsoNormal> </p>
+ </td>
+ </tr>
+ <tr style='height:6.25pt'>
+ <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>version</span></p>
+ </td>
+ <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>no</p>
+ </td>
+ <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+ height:6.25pt'>
+ <p class=MsoNormal>Write version string to stdout and exit.</p>
+ </td>
+ </tr>
+</table>
+
+<p class=MsoNormal><i> </i></p>
+
+<p class=MsoNormal><i>Notes</i></p>
+
+<p class=MsoNormal>[1] Default depends on the profile scoring function. To
+determine the default, use –<i>verbose –log</i> and check the log file.</p>
+
+<p class=MsoNormal><u><span style='text-decoration:none'> </span></u></p>
+
+</div>
+
+</body>
+
+</html>
Added: trunk/packages/muscle/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/muscle/trunk/debian/patches/Makefile (rev 0)
+++ trunk/packages/muscle/trunk/debian/patches/Makefile 2008-01-12 07:15:13 UTC (rev 1123)
@@ -0,0 +1,37 @@
+Index: muscle3.6_src/Makefile
+===================================================================
+--- muscle3.6_src.orig/Makefile
++++ muscle3.6_src/Makefile
+@@ -9,9 +9,9 @@
+ # On OSX, using -static gives the error "ld: can't locate file for: -lcrt0.o",
+ # this is fixed by deleting "-static" from the LDLIBS line.
+
+-CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
+-LDLIBS = -lm -static
+-# LDLIBS = -lm
++CFLAGS = -O2 -funroll-loops -Winline -DNDEBUG=1
++# LDLIBS = -lm -static
++LDLIBS = -lm
+
+ OBJ = .o
+ EXE =
+@@ -34,3 +34,19 @@
+ muscle: $(CPPOBJ)
+ $(LD) -o muscle $(CPPOBJ) $(LDLIBS)
+ strip muscle
++
++DESTDIR=""
++
++install: muscle
++ if [ ! -x $(DESTDIR)/usr/bin ]; then mkdir -p $(DESTDIR)/usr/bin; fi
++ cp muscle $(DESTDIR)/usr/bin/muscle
++
++install-doc: debian/muscle.html
++ if [ ! -x $(DESTDIR)/usr/share/doc/muscle ]; then mkdir -p $(DESTDIR)/usr/share/doc/muscle; fi
++ if [ ! -x $(DESTDIR)/usr/share/doc/muscle-doc ]; then mkdir -p $(DESTDIR)/usr/share/doc/muscle-doc; fi
++ cp debian/muscle.html $(DESTDIR)/usr/share/doc/muscle/
++ (cd $(DESTDIR)/usr/share/doc/muscle-doc/ && ln -s ../muscle/muscle.html* . )
++
++clean:
++ $(RM) *.o make.err make.out
++ $(RM) muscle
Modified: trunk/packages/muscle/trunk/debian/rules
===================================================================
--- trunk/packages/muscle/trunk/debian/rules 2008-01-12 06:43:59 UTC (rev 1122)
+++ trunk/packages/muscle/trunk/debian/rules 2008-01-12 07:15:13 UTC (rev 1123)
@@ -6,6 +6,8 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+include /usr/share/quilt/quilt.make
+
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
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