[med-svn] r2239 - trunk/packages/emboss/trunk/debian/manpages
plessy at alioth.debian.org
plessy at alioth.debian.org
Wed Jul 16 06:03:18 UTC 2008
Author: plessy
Date: 2008-07-16 06:03:16 +0000 (Wed, 16 Jul 2008)
New Revision: 2239
Added:
trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e
trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e
trunk/packages/emboss/trunk/debian/manpages/consambig.1e
trunk/packages/emboss/trunk/debian/manpages/density.1e
trunk/packages/emboss/trunk/debian/manpages/featcopy.1e
trunk/packages/emboss/trunk/debian/manpages/featreport.1e
trunk/packages/emboss/trunk/debian/manpages/infobase.1e
trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e
trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e
trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e
trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e
trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e
trunk/packages/emboss/trunk/debian/manpages/nohtml.1e
trunk/packages/emboss/trunk/debian/manpages/nospace.1e
trunk/packages/emboss/trunk/debian/manpages/notab.1e
trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e
trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e
trunk/packages/emboss/trunk/debian/manpages/trimspace.1e
Modified:
trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e
trunk/packages/emboss/trunk/debian/manpages/abiview.1e
trunk/packages/emboss/trunk/debian/manpages/acdc.1e
trunk/packages/emboss/trunk/debian/manpages/acdlog.1e
trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e
trunk/packages/emboss/trunk/debian/manpages/acdtable.1e
trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e
trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e
trunk/packages/emboss/trunk/debian/manpages/ajbad.1e
trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e
trunk/packages/emboss/trunk/debian/manpages/ajtest.1e
trunk/packages/emboss/trunk/debian/manpages/antigenic.1e
trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e
trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e
trunk/packages/emboss/trunk/debian/manpages/banana.1e
trunk/packages/emboss/trunk/debian/manpages/biosed.1e
trunk/packages/emboss/trunk/debian/manpages/btwisted.1e
trunk/packages/emboss/trunk/debian/manpages/cai.1e
trunk/packages/emboss/trunk/debian/manpages/chaos.1e
trunk/packages/emboss/trunk/debian/manpages/charge.1e
trunk/packages/emboss/trunk/debian/manpages/checktrans.1e
trunk/packages/emboss/trunk/debian/manpages/chips.1e
trunk/packages/emboss/trunk/debian/manpages/cirdna.1e
trunk/packages/emboss/trunk/debian/manpages/codcmp.1e
trunk/packages/emboss/trunk/debian/manpages/codcopy.1e
trunk/packages/emboss/trunk/debian/manpages/coderet.1e
trunk/packages/emboss/trunk/debian/manpages/complex.1e
trunk/packages/emboss/trunk/debian/manpages/compseq.1e
trunk/packages/emboss/trunk/debian/manpages/cons.1e
trunk/packages/emboss/trunk/debian/manpages/corbatest.1e
trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e
trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e
trunk/packages/emboss/trunk/debian/manpages/cusp.1e
trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e
trunk/packages/emboss/trunk/debian/manpages/cutseq.1e
trunk/packages/emboss/trunk/debian/manpages/dan.1e
trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e
trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e
trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e
trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e
trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e
trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e
trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e
trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e
trunk/packages/emboss/trunk/debian/manpages/degapseq.1e
trunk/packages/emboss/trunk/debian/manpages/demoalign.1e
trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e
trunk/packages/emboss/trunk/debian/manpages/demolist.1e
trunk/packages/emboss/trunk/debian/manpages/demoreport.1e
trunk/packages/emboss/trunk/debian/manpages/demosequence.1e
trunk/packages/emboss/trunk/debian/manpages/demostring.1e
trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e
trunk/packages/emboss/trunk/debian/manpages/demotable.1e
trunk/packages/emboss/trunk/debian/manpages/descseq.1e
trunk/packages/emboss/trunk/debian/manpages/diffseq.1e
trunk/packages/emboss/trunk/debian/manpages/digest.1e
trunk/packages/emboss/trunk/debian/manpages/distmat.1e
trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e
trunk/packages/emboss/trunk/debian/manpages/dotpath.1e
trunk/packages/emboss/trunk/debian/manpages/dottup.1e
trunk/packages/emboss/trunk/debian/manpages/dreg.1e
trunk/packages/emboss/trunk/debian/manpages/edialign.1e
trunk/packages/emboss/trunk/debian/manpages/einverted.1e
trunk/packages/emboss/trunk/debian/manpages/embossdata.1e
trunk/packages/emboss/trunk/debian/manpages/embossversion.1e
trunk/packages/emboss/trunk/debian/manpages/emma.1e
trunk/packages/emboss/trunk/debian/manpages/emowse.1e
trunk/packages/emboss/trunk/debian/manpages/entrails.1e
trunk/packages/emboss/trunk/debian/manpages/entret.1e
trunk/packages/emboss/trunk/debian/manpages/epestfind.1e
trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e
trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e
trunk/packages/emboss/trunk/debian/manpages/est2genome.1e
trunk/packages/emboss/trunk/debian/manpages/etandem.1e
trunk/packages/emboss/trunk/debian/manpages/extractalign.1e
trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e
trunk/packages/emboss/trunk/debian/manpages/extractseq.1e
trunk/packages/emboss/trunk/debian/manpages/findkm.1e
trunk/packages/emboss/trunk/debian/manpages/freak.1e
trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e
trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e
trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e
trunk/packages/emboss/trunk/debian/manpages/garnier.1e
trunk/packages/emboss/trunk/debian/manpages/geecee.1e
trunk/packages/emboss/trunk/debian/manpages/getorf.1e
trunk/packages/emboss/trunk/debian/manpages/giep.1e
trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e
trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e
trunk/packages/emboss/trunk/debian/manpages/hmoment.1e
trunk/packages/emboss/trunk/debian/manpages/iep.1e
trunk/packages/emboss/trunk/debian/manpages/infoalign.1e
trunk/packages/emboss/trunk/debian/manpages/infoseq.1e
trunk/packages/emboss/trunk/debian/manpages/intconv.1e
trunk/packages/emboss/trunk/debian/manpages/isochore.1e
trunk/packages/emboss/trunk/debian/manpages/lindna.1e
trunk/packages/emboss/trunk/debian/manpages/listor.1e
trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e
trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e
trunk/packages/emboss/trunk/debian/manpages/marscan.1e
trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e
trunk/packages/emboss/trunk/debian/manpages/maskseq.1e
trunk/packages/emboss/trunk/debian/manpages/matcher.1e
trunk/packages/emboss/trunk/debian/manpages/megamerger.1e
trunk/packages/emboss/trunk/debian/manpages/merger.1e
trunk/packages/emboss/trunk/debian/manpages/msbar.1e
trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e
trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e
trunk/packages/emboss/trunk/debian/manpages/needle.1e
trunk/packages/emboss/trunk/debian/manpages/newcoils.1e
trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e
trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e
trunk/packages/emboss/trunk/debian/manpages/newseq.1e
trunk/packages/emboss/trunk/debian/manpages/noreturn.1e
trunk/packages/emboss/trunk/debian/manpages/notseq.1e
trunk/packages/emboss/trunk/debian/manpages/nthseq.1e
trunk/packages/emboss/trunk/debian/manpages/octanol.1e
trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e
trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e
trunk/packages/emboss/trunk/debian/manpages/origunion.1e
trunk/packages/emboss/trunk/debian/manpages/palindrome.1e
trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e
trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e
trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e
trunk/packages/emboss/trunk/debian/manpages/patmattest.1e
trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e
trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e
trunk/packages/emboss/trunk/debian/manpages/pepnet.1e
trunk/packages/emboss/trunk/debian/manpages/pepstats.1e
trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e
trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e
trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e
trunk/packages/emboss/trunk/debian/manpages/plotcon.1e
trunk/packages/emboss/trunk/debian/manpages/plotorf.1e
trunk/packages/emboss/trunk/debian/manpages/polydot.1e
trunk/packages/emboss/trunk/debian/manpages/preg.1e
trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e
trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e
trunk/packages/emboss/trunk/debian/manpages/prima.1e
trunk/packages/emboss/trunk/debian/manpages/primers.1e
trunk/packages/emboss/trunk/debian/manpages/primersearch.1e
trunk/packages/emboss/trunk/debian/manpages/printsextract.1e
trunk/packages/emboss/trunk/debian/manpages/profit.1e
trunk/packages/emboss/trunk/debian/manpages/prophecy.1e
trunk/packages/emboss/trunk/debian/manpages/prophet.1e
trunk/packages/emboss/trunk/debian/manpages/prosextract.1e
trunk/packages/emboss/trunk/debian/manpages/pscan.1e
trunk/packages/emboss/trunk/debian/manpages/psiphi.1e
trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e
trunk/packages/emboss/trunk/debian/manpages/recoder.1e
trunk/packages/emboss/trunk/debian/manpages/redata.1e
trunk/packages/emboss/trunk/debian/manpages/remap.1e
trunk/packages/emboss/trunk/debian/manpages/restover.1e
trunk/packages/emboss/trunk/debian/manpages/restrict.1e
trunk/packages/emboss/trunk/debian/manpages/revseq.1e
trunk/packages/emboss/trunk/debian/manpages/seealso.1e
trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e
trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e
trunk/packages/emboss/trunk/debian/manpages/seqret.1e
trunk/packages/emboss/trunk/debian/manpages/seqretall.1e
trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e
trunk/packages/emboss/trunk/debian/manpages/seqretset.1e
trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e
trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e
trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e
trunk/packages/emboss/trunk/debian/manpages/showalign.1e
trunk/packages/emboss/trunk/debian/manpages/showdb.1e
trunk/packages/emboss/trunk/debian/manpages/showfeat.1e
trunk/packages/emboss/trunk/debian/manpages/showorf.1e
trunk/packages/emboss/trunk/debian/manpages/showseq.1e
trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e
trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e
trunk/packages/emboss/trunk/debian/manpages/silent.1e
trunk/packages/emboss/trunk/debian/manpages/sirna.1e
trunk/packages/emboss/trunk/debian/manpages/sixpack.1e
trunk/packages/emboss/trunk/debian/manpages/skipseq.1e
trunk/packages/emboss/trunk/debian/manpages/splitter.1e
trunk/packages/emboss/trunk/debian/manpages/stretcher.1e
trunk/packages/emboss/trunk/debian/manpages/stssearch.1e
trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e
trunk/packages/emboss/trunk/debian/manpages/syco.1e
trunk/packages/emboss/trunk/debian/manpages/tcode.1e
trunk/packages/emboss/trunk/debian/manpages/testplot.1e
trunk/packages/emboss/trunk/debian/manpages/textsearch.1e
trunk/packages/emboss/trunk/debian/manpages/tfextract.1e
trunk/packages/emboss/trunk/debian/manpages/tfm.1e
trunk/packages/emboss/trunk/debian/manpages/tfscan.1e
trunk/packages/emboss/trunk/debian/manpages/tmap.1e
trunk/packages/emboss/trunk/debian/manpages/tranalign.1e
trunk/packages/emboss/trunk/debian/manpages/transeq.1e
trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e
trunk/packages/emboss/trunk/debian/manpages/trimest.1e
trunk/packages/emboss/trunk/debian/manpages/trimseq.1e
trunk/packages/emboss/trunk/debian/manpages/twofeat.1e
trunk/packages/emboss/trunk/debian/manpages/union.1e
trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e
trunk/packages/emboss/trunk/debian/manpages/water.1e
trunk/packages/emboss/trunk/debian/manpages/whichdb.1e
trunk/packages/emboss/trunk/debian/manpages/wobble.1e
trunk/packages/emboss/trunk/debian/manpages/wordcount.1e
trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e
trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e
trunk/packages/emboss/trunk/debian/manpages/wossname.1e
trunk/packages/emboss/trunk/debian/manpages/yank.1e
Log:
Regenerated the manual pages.
Modified: trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: AAINDEXEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "AAINDEXEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "AAINDEXEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-aaindexextract \- Extract data from AAINDEX
+aaindexextract \- Extract amino acid property data from AAINDEX
.SH "SYNOPSIS"
.HP 15
\fBaaindexextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/abiview.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/abiview.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/abiview.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ABIVIEW
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ABIVIEW" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ABIVIEW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-abiview \- Reads ABI file and display the trace
+abiview \- Display the trace in an ABI sequencer file
.SH "SYNOPSIS"
.HP 8
\fBabiview\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-startbase\ \fR\fB\fIinteger\fR\fR] [\fB\-endbase\ \fR\fB\fIinteger\fR\fR] \fB\-separate\ \fR\fB\fIboolean\fR\fR [\fB\-yticks\ \fR\fB\fIboolean\fR\fR] [\fB\-sequence\ \fR\fB\fIboolean\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-bases\ \fR\fB\fIstring\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/acdc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdc.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdc.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDC
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDC" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdc \- ACD compiler
+acdc \- Test an application ACD file
.SH "SYNOPSIS"
.HP 5
\fBacdc\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/acdlog.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdlog.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdlog.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDLOG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDLOG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDLOG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdlog \- ACD compiler logging
+acdlog \- Test application ACD file processing and trace data structures
.SH "SYNOPSIS"
.HP 7
\fBacdlog\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDPRETTY
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDPRETTY" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDPRETTY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdpretty \- ACD pretty printing utility
+acdpretty \- Correctly reformat an application ACD file
.SH "SYNOPSIS"
.HP 10
\fBacdpretty\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/acdtable.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdtable.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdtable.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDTABLE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDTABLE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDTABLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdtable \- Creates an HTML table from an ACD file
+acdtable \- Generate an HTML table of parameters from an application ACD file
.SH "SYNOPSIS"
.HP 9
\fBacdtable\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDTRACE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDTRACE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDTRACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdtrace \- ACD compiler on-screen trace
+acdtrace \- Trace processing of an application ACD file (for testing)
.SH "SYNOPSIS"
.HP 9
\fBacdtrace\fR \fB\-program\ \fR\fB\fIstring\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ACDVALID
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ACDVALID" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ACDVALID" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-acdvalid \- ACD file validation
+acdvalid \- Validate an application ACD file
.SH "SYNOPSIS"
.HP 9
\fBacdvalid\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/ajbad.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajbad.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/ajbad.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: AJBAD
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "AJBAD" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "AJBAD" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: AJFEATEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "AJFEATEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "AJFEATEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/ajtest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajtest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/ajtest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: AJTEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "AJTEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "AJTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Added: trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,71 @@
+.\" Title: ALIGNCOPY
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "ALIGNCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+aligncopy \- Reads and writes alignments
+.SH "SYNOPSIS"
+.HP 10
+\fBaligncopy\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP 10
+\fBaligncopy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBaligncopy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-comment\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-append\fR \fIboolean\fR
+.RS 4
+This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+aligncopy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,71 @@
+.\" Title: ALIGNCOPYPAIR
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "ALIGNCOPYPAIR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+aligncopypair \- Reads and writes pairs from alignments
+.SH "SYNOPSIS"
+.HP 14
+\fBaligncopypair\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP 14
+\fBaligncopypair\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBaligncopypair\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-comment\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-append\fR \fIboolean\fR
+.RS 4
+This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+aligncopypair is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/antigenic.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/antigenic.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/antigenic.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: ANTIGENIC
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ANTIGENIC" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ANTIGENIC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: BACKTRANAMBIG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "BACKTRANAMBIG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "BACKTRANAMBIG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-backtranambig \- Back translate a protein sequence to ambiguous codons
+backtranambig \- Back-translate a protein sequence to ambiguous nucleotide sequence
.SH "SYNOPSIS"
.HP 14
\fBbacktranambig\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: BACKTRANSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "BACKTRANSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "BACKTRANSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-backtranseq \- Back translate a protein sequence
+backtranseq \- Back-translate a protein sequence to a nucleotide sequence
.SH "SYNOPSIS"
.HP 12
\fBbacktranseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-cfile\ \fR\fB\fIcodon\fR\fR] \fB\-outfile\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/banana.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/banana.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/banana.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: BANANA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "BANANA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "BANANA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-banana \- Bending and curvature plot in B-DNA
+banana \- Plot bending and curvature data for B-DNA
.SH "SYNOPSIS"
.HP 7
\fBbanana\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-anglesfile\ \fR\fB\fIdatafile\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/biosed.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/biosed.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/biosed.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: BIOSED
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "BIOSED" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "BIOSED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/btwisted.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/btwisted.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/btwisted.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: BTWISTED
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "BTWISTED" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "BTWISTED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-btwisted \- Calculates the twisting in a B-DNA sequence
+btwisted \- Calculate the twisting in a B-DNA sequence
.SH "SYNOPSIS"
.HP 9
\fBbtwisted\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-angledata\ \fR\fB\fIdatafile\fR\fR \fB\-energydata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cai.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cai.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cai.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CAI
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CAI" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CAI" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cai \- CAI codon adaptation index
+cai \- Calculate codon adaptation index
.SH "SYNOPSIS"
.HP 4
\fBcai\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/chaos.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/chaos.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/chaos.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CHAOS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CHAOS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CHAOS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-chaos \- Create a chaos game representation plot for a sequence
+chaos \- Draw a chaos game representation plot for a nucleotide sequence
.SH "SYNOPSIS"
.HP 6
\fBchaos\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/charge.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/charge.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/charge.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CHARGE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CHARGE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CHARGE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-charge \- Protein charge plot
+charge \- Draw a protein charge plot
.SH "SYNOPSIS"
.HP 7
\fBcharge\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/checktrans.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/checktrans.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/checktrans.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: CHECKTRANS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CHECKTRANS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CHECKTRANS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/chips.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/chips.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/chips.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CHIPS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CHIPS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CHIPS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-chips \- Codon usage statistics
+chips \- Calculates Nc codon usage statistic
.SH "SYNOPSIS"
.HP 6
\fBchips\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-sum\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cirdna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cirdna.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cirdna.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: CIRDNA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CIRDNA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CIRDNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/codcmp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/codcmp.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/codcmp.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: CODCMP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CODCMP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CODCMP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/codcopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/codcopy.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/codcopy.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CODCOPY
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CODCOPY" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CODCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-codcopy \- Reads and writes a codon usage table
+codcopy \- Copy and reformat a codon usage table
.SH "SYNOPSIS"
.HP 8
\fBcodcopy\fR \fB\-infile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutcodon\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/coderet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/coderet.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/coderet.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: CODERET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CODERET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CODERET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/complex.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/complex.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/complex.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: COMPLEX
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "COMPLEX" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "COMPLEX" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/compseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/compseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/compseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: COMPSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "COMPSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "COMPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-compseq \- Count composition of dimer/trimer/etc words in a sequence
+compseq \- Calculate the composition of unique words in sequences
.SH "SYNOPSIS"
.HP 8
\fBcompseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-infile\ \fR\fB\fIinfile\fR\fR] \fB\-word\ \fR\fB\fIinteger\fR\fR [\fB\-frame\ \fR\fB\fIinteger\fR\fR] \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR [\fB\-calcfreq\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-zerocount\ \fR\fB\fIboolean\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/cons.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cons.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cons.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CONS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CONS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CONS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cons \- Creates a consensus from multiple alignments
+cons \- Create a consensus sequence from a multiple alignment
.SH "SYNOPSIS"
.HP 5
\fBcons\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-setcase\ \fR\fB\fIfloat\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR]
Added: trunk/packages/emboss/trunk/debian/manpages/consambig.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/consambig.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/consambig.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,60 @@
+.\" Title: CONSAMBIG
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "CONSAMBIG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+consambig \- Create an ambiguous consensus sequence from a multiple alignment
+.SH "SYNOPSIS"
+.HP 10
+\fBconsambig\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR]
+.HP 10
+\fBconsambig\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBconsambig\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Additional section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+consambig is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/corbatest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/corbatest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/corbatest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: CORBATEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CORBATEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CORBATEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CPGPLOT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CPGPLOT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CPGPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cpgplot \- Plot CpG rich areas
+cpgplot \- Identify and plot CpG islands in nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 8
\fBcpgplot\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-obsexp\ \fR\fB\fIboolean\fR\fR \fB\-cg\ \fR\fB\fIboolean\fR\fR \fB\-pc\ \fR\fB\fIboolean\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CPGREPORT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CPGREPORT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CPGREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cpgreport \- Reports all CpG rich regions
+cpgreport \- Identify and report CpG-rich regions in nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 10
\fBcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cusp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cusp.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cusp.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CUSP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CUSP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CUSP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cusp \- Create a codon usage table
+cusp \- Create a codon usage table from nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 5
\fBcusp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CUTGEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CUTGEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CUTGEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cutgextract \- Extract data from CUTG
+cutgextract \- Extract codon usage tables from from CUTG database
.SH "SYNOPSIS"
.HP 12
\fBcutgextract\fR \fB\-directory\ \fR\fB\fIdirlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-wildspec\ \fR\fB\fIstring\fR\fR \fB\-species\ \fR\fB\fIstring\fR\fR \fB\-allrecords\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/cutseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cutseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/cutseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: CUTSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "CUTSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "CUTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-cutseq \- Removes a specified section from a sequence.
+cutseq \- Removes a section from a sequence
.SH "SYNOPSIS"
.HP 7
\fBcutseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-from\ \fR\fB\fIinteger\fR\fR \fB\-to\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dan.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dan.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DAN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DAN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dan \- Calculates DNA RNA/DNA melting temperature
+dan \- Calculates nucleic acid melting temperature
.SH "SYNOPSIS"
.HP 4
\fBdan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-windowsize\ \fR\fB\fIinteger\fR\fR \fB\-shiftincrement\ \fR\fB\fIinteger\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR [\fB\-product\ \fR\fB\fItoggle\fR\fR] \fB\-formamide\ \fR\fB\fIfloat\fR\fR \fB\-mismatch\ \fR\fB\fIfloat\fR\fR \fB\-prodlen\ \fR\fB\fIinteger\fR\fR [\fB\-thermo\ \fR\fB\fItoggle\fR\fR] \fB\-temperature\ \fR\fB\fIfloat\fR\fR \fB\-rna\ \fR\fB\fIboolean\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-mintemp\ \fR\fB\fIfloat\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DBIBLAST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBIBLAST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBIBLAST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DBIFASTA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBIFASTA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBIFASTA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dbifasta \- Database indexing for fasta file databases
+dbifasta \- Index a fasta file database
.SH "SYNOPSIS"
.HP 9
\fBdbifasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DBIFLAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBIFLAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBIFLAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DBIGCG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBIGCG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBIGCG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: DBXFASTA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBXFASTA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBXFASTA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dbxfasta \- Database b+tree indexing for fasta file databases
+dbxfasta \- Index a fasta file database using b+tree indices
.SH "SYNOPSIS"
.HP 9
-\fBdbxfasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+\fBdbxfasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 9
\fBdbxfasta\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -44,10 +44,16 @@
.PP
\fB\-filenames\fR \fIstring\fR
.RS 4
-Default value: *\&.dat
+Default value: *\&.fasta
.RE
.SS "Required section"
.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: id,acc
+.RE
+.SS "Advanced section"
+.PP
\fB\-release\fR \fIstring\fR
.RS 4
Default value: 0\&.0
@@ -57,13 +63,7 @@
.RS 4
Default value: 00/00/00
.RE
-.SS "Advanced section"
.PP
-\fB\-fields\fR \fIlist\fR
-.RS 4
-Default value: id,acc
-.RE
-.PP
\fB\-exclude\fR \fIstring\fR
.RS 4
.RE
@@ -73,6 +73,10 @@
.RS 4
Default value: \&.
.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
Modified: trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: DBXFLAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBXFLAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBXFLAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dbxflat \- Database b+tree indexing for flat file databases
+dbxflat \- Index a flat file database using b+tree indices
.SH "SYNOPSIS"
.HP 8
-\fBdbxflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+\fBdbxflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 8
\fBdbxflat\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -73,6 +73,10 @@
.RS 4
Default value: \&.
.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
Modified: trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: DBXGCG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBXGCG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBXGCG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dbxgcg \- Database b+tree indexing for GCG formatted databases
+dbxgcg \- Index a GCG formatted database using b+tree indices
.SH "SYNOPSIS"
.HP 7
-\fBdbxgcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+\fBdbxgcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 7
\fBdbxgcg\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -73,6 +73,10 @@
.RS 4
Default value: \&.
.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
Modified: trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DBXSTAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DBXSTAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DBXSTAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -14,7 +14,7 @@
dbxstat \- Dump statistics for dbx databases
.SH "SYNOPSIS"
.HP 8
-\fBdbxstat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIstring\fR\fR \fB\-idtype\ \fR\fB\fIlist\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+\fBdbxstat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-idtype\ \fR\fB\fIlist\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 8
\fBdbxstat\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -28,7 +28,7 @@
.RS 4
.RE
.PP
-\fB\-indexdir\fR \fIstring\fR
+\fB\-indexdir\fR \fIdirectory\fR
.RS 4
Default value: \&.
.RE
Modified: trunk/packages/emboss/trunk/debian/manpages/degapseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/degapseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/degapseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DEGAPSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEGAPSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEGAPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-degapseq \- Removes gap characters from sequences
+degapseq \- Removes non-alphabetic (e.g. gap) characters from sequences
.SH "SYNOPSIS"
.HP 9
\fBdegapseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/demoalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demoalign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demoalign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOFEATURES
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOFEATURES" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOFEATURES" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demolist.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demolist.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demolist.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOLIST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOLIST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOLIST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demoreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demoreport.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demoreport.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOREPORT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOREPORT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demosequence.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demosequence.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demosequence.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOSEQUENCE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOSEQUENCE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSEQUENCE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demostring.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demostring.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demostring.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOSTRING
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOSTRING" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSTRING" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOSTRINGNEW
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOSTRINGNEW" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSTRINGNEW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/demotable.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demotable.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/demotable.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DEMOTABLE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DEMOTABLE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOTABLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Added: trunk/packages/emboss/trunk/debian/manpages/density.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/density.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/density.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,78 @@
+.\" Title: DENSITY
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "DENSITY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+density \- Draw a nucleic acid density plot
+.SH "SYNOPSIS"
+.HP 8
+\fBdensity\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-quad\ \fR\fB\fItoggle\fR\fR \fB\-dual\ \fR\fB\fItoggle\fR\fR \fB\-qgraph\ \fR\fB\fIxygraph\fR\fR \fB\-dgraph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP 8
+\fBdensity\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdensity\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.SS "Output section"
+.PP
+\fB\-quad\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dual\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-qgraph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-dgraph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+density is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/descseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/descseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/descseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DESCSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DESCSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DESCSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/diffseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/diffseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/diffseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DIFFSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DIFFSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DIFFSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-diffseq \- Find differences between nearly identical sequences
+diffseq \- Compare and report features of two similar sequences
.SH "SYNOPSIS"
.HP 8
\fBdiffseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-globaldifferences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/digest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/digest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/digest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: DIGEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DIGEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DIGEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-digest \- Protein proteolytic enzyme or reagent cleavage digest
+digest \- Reports on protein proteolytic enzyme or reagent cleavage sites
.SH "SYNOPSIS"
.HP 7
-\fBdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+\fBdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
.HP 7
\fBdigest\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -28,9 +28,9 @@
.RS 4
.RE
.PP
-\fB\-aadata\fR \fIdatafile\fR
+\fB\-mwdata\fR \fIdatafile\fR
.RS 4
-Molecular weight data for amino acids Default value: Eamino\&.dat
+Molecular weight data for amino acids Default value: Emolwt\&.dat
.RE
.SS "Required section"
.PP
@@ -38,11 +38,16 @@
.RS 4
Default value: 1
.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
.SS "Advanced section"
.PP
\fB\-unfavoured\fR \fIboolean\fR
.RS 4
-Trypsin will not normally cut after a K if it is followed by (e\&.g\&.) another K or a P\&. Specifying this shows those cuts\&. as well as the favoured ones\&.
+Trypsin will not normally cut after \'KR\' if they are followed by any of \'KRIFLP\'\&. Lys\-C will not normally cut after \'K\' if it is followed by \'P\'\&. Arg\-C will not normally cut after \'R\' if it is followed by \'P\'\&. V8\-bicarb will not normally cut after \'E\' if it is followed by any of \'KREP\'\&. V8\-phosph will not normally cut after \'DE\' if they are followed by \'P\'\&. Chymotrypsin will not normally cut after \'FYWLM\' if they are followed by \'P\'\&. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones\&.
.RE
.PP
\fB\-ragging\fR \fIboolean\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/distmat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/distmat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/distmat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DISTMAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DISTMAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DISTMAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-distmat \- Creates a distance matrix from multiple alignments
+distmat \- Create a distance matrix from a multiple sequence alignment
.SH "SYNOPSIS"
.HP 8
\fBdistmat\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-nucmethod\ \fR\fB\fIlist\fR\fR \fB\-protmethod\ \fR\fB\fIlist\fR\fR \fB\-ambiguous\ \fR\fB\fIboolean\fR\fR \fB\-gapweight\ \fR\fB\fIfloat\fR\fR \fB\-position\ \fR\fB\fIinteger\fR\fR \fB\-calculatea\ \fR\fB\fIboolean\fR\fR \fB\-parametera\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DOTMATCHER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DOTMATCHER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DOTMATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dotmatcher \- Displays a thresholded dotplot of two sequences
+dotmatcher \- Draw a threshold dotplot of two sequences
.SH "SYNOPSIS"
.HP 11
\fBdotmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-windowsize\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIinteger\fR\fR] \fB\-stretch\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-xygraph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dotpath.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dotpath.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dotpath.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DOTPATH
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DOTPATH" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DOTPATH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dotpath \- Non-overlapping wordmatch dotplot of two sequences
+dotpath \- Draw a non-overlapping wordmatch dotplot of two sequences
.SH "SYNOPSIS"
.HP 8
\fBdotpath\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-overlaps\ \fR\fB\fIboolean\fR\fR] [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/dottup.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dottup.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dottup.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: DOTTUP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DOTTUP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DOTTUP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/dreg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dreg.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/dreg.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: DREG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "DREG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "DREG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dreg \- Regular expression search of a nucleotide sequence
+dreg \- Regular expression search of nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 5
\fBdreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/edialign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/edialign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/edialign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: EDIALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EDIALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EDIALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/einverted.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/einverted.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/einverted.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EINVERTED
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EINVERTED" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EINVERTED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-einverted \- Finds DNA inverted repeats
+einverted \- Finds inverted repeats in nucleotide sequences
.SH "SYNOPSIS"
.HP 10
\fBeinverted\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-match\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/embossdata.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/embossdata.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/embossdata.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EMBOSSDATA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EMBOSSDATA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EMBOSSDATA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-embossdata \- Finds or fetches data files read by EMBOSS programs
+embossdata \- Find and retrieve EMBOSS data files
.SH "SYNOPSIS"
.HP 11
\fBembossdata\fR [\fB\-showall\ \fR\fB\fItoggle\fR\fR] \fB\-fetch\ \fR\fB\fIboolean\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR \fB\-reject\ \fR\fB\fIselection\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/embossversion.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/embossversion.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/embossversion.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EMBOSSVERSION
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EMBOSSVERSION" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EMBOSSVERSION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-embossversion \- Writes the current EMBOSS version number
+embossversion \- Writes the current EMBOSS version number to a file
.SH "SYNOPSIS"
.HP 14
\fBembossversion\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/emma.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/emma.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/emma.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EMMA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EMMA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EMMA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-emma \- Multiple alignment program - interface to ClustalW program
+emma \- Multiple sequence alignment (ClustalW wrapper)
.SH "SYNOPSIS"
.HP 5
\fBemma\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-onlydend\ \fR\fB\fItoggle\fR\fR] \fB\-dend\ \fR\fB\fItoggle\fR\fR \fB\-dendfile\ \fR\fB\fIinfile\fR\fR \fB\-pwmatrix\ \fR\fB\fIlist\fR\fR \fB\-pwdnamatrix\ \fR\fB\fIlist\fR\fR \fB\-usermatrix\ \fR\fB\fIvariable\fR\fR \fB\-pairwisedatafile\ \fR\fB\fIinfile\fR\fR \fB\-matrix\ \fR\fB\fIlist\fR\fR \fB\-usermamatrix\ \fR\fB\fIvariable\fR\fR \fB\-dnamatrix\ \fR\fB\fIlist\fR\fR \fB\-umamatrix\ \fR\fB\fIvariable\fR\fR \fB\-mamatrixfile\ \fR\fB\fIinfile\fR\fR [\fB\-slow\ \fR\fB\fItoggle\fR\fR] \fB\-pwgapopen\ \fR\fB\fIfloat\fR\fR \fB\-pwgapextend\ \fR\fB\fIfloat\fR\fR \fB\-ktup\ \fR\fB\fIinteger\fR\fR \fB\-gapw\ \fR\fB\fIinteger\fR\fR \fB\-topdiags\ \fR\fB\fIinteger\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-nopercent\ \fR\fB\fIboolean\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-endgaps\ \fR\fB\fIboolean\fR\fR] [\fB\-gapdist\ \fR\fB\fIinteger\fR\fR] \fB\-norgap\ \fR\fB\fIboolean\fR\fR \fB\-hgapres\ \fR\fB\fIstring\fR\fR \fB\-nohgap\ \fR\fB\fIboolean\fR\fR [\fB\-maxdiv\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR \fB\-dendoutfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/emowse.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/emowse.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/emowse.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: EMOWSE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EMOWSE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EMOWSE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-emowse \- Protein identification by mass spectrometry
+emowse \- Search protein sequences by digest fragment molecular weight
.SH "SYNOPSIS"
.HP 7
-\fBemowse\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-frequencies\ \fR\fB\fIdatafile\fR\fR \fB\-weight\ \fR\fB\fIinteger\fR\fR \fB\-enzyme\ \fR\fB\fIlist\fR\fR \fB\-pcrange\ \fR\fB\fIinteger\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-partials\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+\fBemowse\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-frequencies\ \fR\fB\fIdatafile\fR\fR \fB\-weight\ \fR\fB\fIinteger\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-enzyme\ \fR\fB\fIlist\fR\fR \fB\-pcrange\ \fR\fB\fIinteger\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-partials\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 7
\fBemowse\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -32,9 +32,9 @@
.RS 4
.RE
.PP
-\fB\-aadata\fR \fIdatafile\fR
+\fB\-mwdata\fR \fIdatafile\fR
.RS 4
-Default value: Eamino\&.dat
+Default value: Emolwt\&.dat
.RE
.PP
\fB\-frequencies\fR \fIdatafile\fR
@@ -46,6 +46,11 @@
\fB\-weight\fR \fIinteger\fR
.RS 4
.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
.SS "Advanced section"
.PP
\fB\-enzyme\fR \fIlist\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/entrails.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/entrails.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/entrails.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: ENTRAILS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ENTRAILS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ENTRAILS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/entret.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/entret.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/entret.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ENTRET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ENTRET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ENTRET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-entret \- Reads and writes (returns) flatfile entries
+entret \- Retrieves sequence entries from flatfile databases and files
.SH "SYNOPSIS"
.HP 7
\fBentret\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/epestfind.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/epestfind.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/epestfind.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: EPESTFIND
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EPESTFIND" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EPESTFIND" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -14,7 +14,7 @@
epestfind \- Finds PEST motifs as potential proteolytic cleavage sites
.SH "SYNOPSIS"
.HP 10
-\fBepestfind\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-aadata\ \fR\fB\fIdatafile\fR\fR] \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-order\ \fR\fB\fIselection\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-potential\ \fR\fB\fIboolean\fR\fR \fB\-poor\ \fR\fB\fIboolean\fR\fR \fB\-invalid\ \fR\fB\fIboolean\fR\fR \fB\-map\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+\fBepestfind\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-mwdata\ \fR\fB\fIdatafile\fR\fR] \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-order\ \fR\fB\fIselection\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-potential\ \fR\fB\fIboolean\fR\fR \fB\-poor\ \fR\fB\fIboolean\fR\fR \fB\-invalid\ \fR\fB\fIboolean\fR\fR \fB\-map\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
.HP 10
\fBepestfind\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -29,9 +29,9 @@
Protein sequence USA to be analysed\&.
.RE
.PP
-\fB\-aadata\fR \fIdatafile\fR
+\fB\-mwdata\fR \fIdatafile\fR
.RS 4
-Default value: Eamino\&.dat
+Default value: Emolwt\&.dat
.RE
.SS "Required section"
.PP
@@ -52,6 +52,11 @@
.RE
.SS "Advanced section"
.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
\fB\-potential\fR \fIboolean\fR
.RS 4
Decide whether potential PEST motifs should be printed\&. Default value: Y
Modified: trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: EPRIMER3
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EPRIMER3" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EPRIMER3" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -110,7 +110,7 @@
.PP
\fB\-otm\fR \fIfloat\fR
.RS 4
-Optimum melting temperature(Celsius) for a primer oligo\&. EPrimer3 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 12, pp 6409\-6412 and Breslauer, Frank, Bloeker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+Optimum melting temperature(Celsius) for a primer oligo\&. EPrimer3 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
.RE
.PP
\fB\-mintm\fR \fIfloat\fR
@@ -150,7 +150,7 @@
.PP
\fB\-dnaconc\fR \fIfloat\fR
.RS 4
-The nanomolar concentration of annealing oligos in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \'c\' in Rychlik, Spencer and Rhoads\' equation (ii) (Nucleic Acids Research, vol 18, num 12) where a suitable value (for a lower initial concentration of template) is \'empirically determined\'\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0
+The nanomolar concentration of annealing oligos in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \'c\' in Rychlik, Spencer and Rhoads\' equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is \'empirically determined\'\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0
.RE
.PP
\fB\-maxpolyx\fR \fIinteger\fR
@@ -213,7 +213,7 @@
.PP
\fB\-oligootm\fR \fIfloat\fR
.RS 4
-Optimum melting temperature (Celsius) for an internal oligo\&. EPrimer3 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 12, pp 6409\-6412 and Breslauer, Frank, Bloeker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+Optimum melting temperature (Celsius) for an internal oligo\&. EPrimer3 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
.RE
.PP
\fB\-oligomintm\fR \fIfloat\fR
@@ -320,7 +320,7 @@
.PP
\fB\-maxendstability\fR \fIfloat\fR
.RS 4
-The maximum stability for the five 3\' bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\' ends\&. The value is the maximum delta G for duplex disruption for the five 3\' bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloeker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. EPrimer3 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \'Selection of Primers for Polymerase Chain Reaction\' in BA White, Ed\&., \'Methods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\', 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0
+The maximum stability for the five 3\' bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\' ends\&. The value is the maximum delta G for duplex disruption for the five 3\' bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. EPrimer3 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \'Selection of Primers for Polymerase Chain Reaction\' in BA White, Ed\&., \'Methods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\', 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0
.RE
.SS "Output section"
.PP
Modified: trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EQUICKTANDEM
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EQUICKTANDEM" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EQUICKTANDEM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-equicktandem \- Finds tandem repeats
+equicktandem \- Finds tandem repeats in nucleotide sequences
.SH "SYNOPSIS"
.HP 13
\fBequicktandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/est2genome.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/est2genome.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/est2genome.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EST2GENOME
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EST2GENOME" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EST2GENOME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-est2genome \- Align EST and genomic DNA sequences
+est2genome \- Align EST sequences to genomic DNA sequence
.SH "SYNOPSIS"
.HP 11
\fBest2genome\fR \fB\-estsequence\ \fR\fB\fIseqall\fR\fR \fB\-genomesequence\ \fR\fB\fIsequence\fR\fR [\fB\-match\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatch\ \fR\fB\fIinteger\fR\fR] [\fB\-gappenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-intronpenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-splicepenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIinteger\fR\fR] \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-splice\ \fR\fB\fIboolean\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-best\ \fR\fB\fIboolean\fR\fR \fB\-space\ \fR\fB\fIfloat\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-align\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/etandem.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/etandem.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/etandem.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ETANDEM
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ETANDEM" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ETANDEM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-etandem \- Looks for tandem repeats in a nucleotide sequence
+etandem \- Finds tandem repeats in a nucleotide sequence
.SH "SYNOPSIS"
.HP 8
\fBetandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-minrepeat\ \fR\fB\fIinteger\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIboolean\fR\fR \fB\-uniform\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/extractalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractalign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/extractalign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: EXTRACTALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EXTRACTALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: EXTRACTFEAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EXTRACTFEAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-extractfeat \- Extract features from a sequence
+extractfeat \- Extract features from sequence(s)
.SH "SYNOPSIS"
.HP 12
\fBextractfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-before\ \fR\fB\fIinteger\fR\fR] [\fB\-after\ \fR\fB\fIinteger\fR\fR] [\fB\-source\ \fR\fB\fIstring\fR\fR] [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-sense\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tag\ \fR\fB\fIstring\fR\fR] [\fB\-value\ \fR\fB\fIstring\fR\fR] [\fB\-join\ \fR\fB\fIboolean\fR\fR] [\fB\-featinname\ \fR\fB\fIboolean\fR\fR] [\fB\-describe\ \fR\fB\fIstring\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/extractseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/extractseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: EXTRACTSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "EXTRACTSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Added: trunk/packages/emboss/trunk/debian/manpages/featcopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/featcopy.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/featcopy.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,54 @@
+.\" Title: FEATCOPY
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "FEATCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+featcopy \- Reads and writes a feature table
+.SH "SYNOPSIS"
+.HP 9
+\fBfeatcopy\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
+.HP 9
+\fBfeatcopy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfeatcopy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-features\fR \fIfeatures\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+featcopy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/featreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/featreport.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/featreport.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,58 @@
+.\" Title: FEATREPORT
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "FEATREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+featreport \- Reads and writes a feature table
+.SH "SYNOPSIS"
+.HP 11
+\fBfeatreport\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP 11
+\fBfeatreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfeatreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-features\fR \fIfeatures\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+featreport is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/findkm.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/findkm.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/findkm.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: FINDKM
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "FINDKM" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "FINDKM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-findkm \- Find Km and Vmax for an enzyme reaction
+findkm \- Calculate and plot enzyme reaction data
.SH "SYNOPSIS"
.HP 7
\fBfindkm\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-plot\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graphlb\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/freak.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/freak.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/freak.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: FREAK
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "FREAK" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "FREAK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-freak \- Residue/base frequency table or plot
+freak \- Generate residue/base frequency table or plot
.SH "SYNOPSIS"
.HP 6
\fBfreak\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-letters\ \fR\fB\fIstring\fR\fR [\fB\-step\ \fR\fB\fIinteger\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: FUZZNUC
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "FUZZNUC" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZNUC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-fuzznuc \- Nucleic acid pattern search
+fuzznuc \- Search for patterns in nucleotide sequences
.SH "SYNOPSIS"
.HP 8
\fBfuzznuc\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: FUZZPRO
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "FUZZPRO" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZPRO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-fuzzpro \- Protein pattern search
+fuzzpro \- Search for patterns in protein sequences
.SH "SYNOPSIS"
.HP 8
\fBfuzzpro\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: FUZZTRAN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "FUZZTRAN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZTRAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-fuzztran \- Protein pattern search after translation
+fuzztran \- Search for patterns in protein sequences (translated)
.SH "SYNOPSIS"
.HP 9
\fBfuzztran\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/garnier.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/garnier.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/garnier.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: GARNIER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "GARNIER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "GARNIER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-garnier \- Predicts protein secondary structure
+garnier \- Predicts protein secondary structure using GOR method
.SH "SYNOPSIS"
.HP 8
\fBgarnier\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-idc\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/geecee.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/geecee.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/geecee.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: GEECEE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "GEECEE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "GEECEE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-geecee \- Calculates fractional GC content of nucleic acid sequences
+geecee \- Calculate fractional GC content of nucleic acid sequences
.SH "SYNOPSIS"
.HP 7
\fBgeecee\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/getorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/getorf.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/getorf.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: GETORF
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "GETORF" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "GETORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/giep.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/giep.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/giep.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: GIEP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "GIEP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "GIEP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: HELIXTURNHELIX
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "HELIXTURNHELIX" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "HELIXTURNHELIX" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-helixturnhelix \- Report nucleic acid binding motifs
+helixturnhelix \- Identify nucleic acid-binding motifs in protein sequences
.SH "SYNOPSIS"
.HP 15
\fBhelixturnhelix\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-mean\ \fR\fB\fIfloat\fR\fR] [\fB\-sd\ \fR\fB\fIfloat\fR\fR] [\fB\-minsd\ \fR\fB\fIfloat\fR\fR] [\fB\-eightyseven\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: HISTOGRAMTEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "HISTOGRAMTEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "HISTOGRAMTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/hmoment.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/hmoment.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/hmoment.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: HMOMENT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "HMOMENT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "HMOMENT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-hmoment \- Hydrophobic moment calculation
+hmoment \- Calculate and plot hydrophobic moment for protein sequence(s)
.SH "SYNOPSIS"
.HP 8
\fBhmoment\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-aangle\ \fR\fB\fIinteger\fR\fR] [\fB\-bangle\ \fR\fB\fIinteger\fR\fR] \fB\-baseline\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-double\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/iep.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/iep.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/iep.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: IEP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "IEP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "IEP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-iep \- Calculates the isoelectric point of a protein
+iep \- Calculate the isoelectric point of proteins
.SH "SYNOPSIS"
.HP 4
\fBiep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-amino\ \fR\fB\fIinteger\fR\fR] [\fB\-termini\ \fR\fB\fIboolean\fR\fR] [\fB\-lysinemodified\ \fR\fB\fIinteger\fR\fR] [\fB\-disulphides\ \fR\fB\fIinteger\fR\fR] \fB\-step\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-report\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/infoalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infoalign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/infoalign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: INFOALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "INFOALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "INFOALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-infoalign \- Information on a multiple sequence alignment
+infoalign \- Display basic information about a multiple sequence alignment
.SH "SYNOPSIS"
.HP 10
\fBinfoalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-seqlength\ \fR\fB\fIboolean\fR\fR \fB\-alignlength\ \fR\fB\fIboolean\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-gapcount\ \fR\fB\fIboolean\fR\fR \fB\-idcount\ \fR\fB\fIboolean\fR\fR \fB\-simcount\ \fR\fB\fIboolean\fR\fR \fB\-diffcount\ \fR\fB\fIboolean\fR\fR \fB\-change\ \fR\fB\fIboolean\fR\fR \fB\-weight\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/infobase.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infobase.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/infobase.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,58 @@
+.\" Title: INFOBASE
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "INFOBASE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+infobase \- Return information on a given nucleotide base
+.SH "SYNOPSIS"
+.HP 9
+\fBinfobase\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 9
+\fBinfobase\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinfobase\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-code\fR \fIstring\fR
+.RS 4
+Enter IUPAC nucleotide base codes, e\&.g\&. A, C, G, T, R, Y etc\&. Default value: ABCDGHKMNRSTUVWXY
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+infobase is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,68 @@
+.\" Title: INFORESIDUE
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "INFORESIDUE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+inforesidue \- Return information on a given amino acid residue
+.SH "SYNOPSIS"
+.HP 12
+\fBinforesidue\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 12
+\fBinforesidue\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinforesidue\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-code\fR \fIstring\fR
+.RS 4
+Enter IUPAC amino acids codes, e\&.g\&. A, C, D, E etc\&. Default value: ABCDEFGHIJKLMNOPQRSTUVWXYZ
+.RE
+.PP
+\fB\-aadata\fR \fIdatafile\fR
+.RS 4
+Amino acid properties Default value: Eamino\&.dat
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+inforesidue is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/infoseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infoseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/infoseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: INFOSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "INFOSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "INFOSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-infoseq \- Displays some simple information about sequences
+infoseq \- Display basic information about sequences
.SH "SYNOPSIS"
.HP 8
\fBinfoseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-columns\ \fR\fB\fIboolean\fR\fR \fB\-delimiter\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-database\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-gi\ \fR\fB\fIboolean\fR\fR \fB\-version\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-length\ \fR\fB\fIboolean\fR\fR \fB\-pgc\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/intconv.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/intconv.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/intconv.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: INTCONV
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "INTCONV" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "INTCONV" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/isochore.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/isochore.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/isochore.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ISOCHORE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ISOCHORE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ISOCHORE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-isochore \- Plots isochores in large DNA sequences
+isochore \- Plots isochores in DNA sequences
.SH "SYNOPSIS"
.HP 9
\fBisochore\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-shift\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,50 @@
+.\" Title: JASPEXTRACT
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "JASPEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+jaspextract \- Extract data from JASPAR
+.SH "SYNOPSIS"
+.HP 12
+\fBjaspextract\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR
+.HP 12
+\fBjaspextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBjaspextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+The directory containing the unzipped and untarred JASPAR_CORE, JASPAR_FAM and JASPAR_PHYLOFACTS subdirectories
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+jaspextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,81 @@
+.\" Title: JASPSCAN
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "JASPSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+jaspscan \- Scans DNA sequences for transcription factors
+.SH "SYNOPSIS"
+.HP 9
+\fBjaspscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-matrices\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-exclude\ \fR\fB\fIstring\fR\fR] [\fB\-both\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP 9
+\fBjaspscan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBjaspscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: C
+.RE
+.PP
+\fB\-matrices\fR \fIstring\fR
+.RS 4
+The name \'all\' reads in all matrix files from the selected JASPAR matrix set\&. You can specify individual matrices by giving their names with commas between then, such as: \'ma0001,ma0015\'\&. The case of the names is not important\&. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a \'@\' character in front of it, for example, \'@matrix\&.list\'\&. Blank lines and lines starting with a hash character or \'!\' are ignored and all other lines are concatenated together with a comma character \',\' and then treated as the list of enzymes to search for\&. An example of a file of matrix names is: ! my matrices ma0001, ma0002 ! other matrices ma0010 ma0032 ma0053 Default value: all
+.RE
+.SS "Required section"
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+If the matrix score is greater than or equal to this percentage then a hit will be reported Default value: 80\&.0
+.RE
+.SS "Additional section"
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+The names of any matrices to exclude from the \'matrices\' list\&. Matrices are specified in the same way as for the selection list\&.
+.RE
+.PP
+\fB\-both\fR \fIboolean\fR
+.RS 4
+If set then both the forward and reverse strands are searched Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+jaspscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/lindna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/lindna.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/lindna.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: LINDNA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "LINDNA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "LINDNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/listor.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/listor.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/listor.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: LISTOR
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "LISTOR" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "LISTOR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MAKENUCSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MAKENUCSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MAKENUCSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-makenucseq \- Creates random nucleotide sequences
+makenucseq \- Create random nucleotide sequences
.SH "SYNOPSIS"
.HP 11
\fBmakenucseq\fR \fB\-codonfile\ \fR\fB\fIcodon\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MAKEPROTSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MAKEPROTSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MAKEPROTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-makeprotseq \- Creates random protein sequences
+makeprotseq \- Create random protein sequences
.SH "SYNOPSIS"
.HP 12
\fBmakeprotseq\fR \fB\-pepstatsfile\ \fR\fB\fIinfile\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/marscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/marscan.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/marscan.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MARSCAN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MARSCAN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MARSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-marscan \- Finds MAR/SAR sites in nucleic sequences
+marscan \- Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
.SH "SYNOPSIS"
.HP 8
\fBmarscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,59 @@
+.\" Title: MASKAMBIGNUC
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "MASKAMBIGNUC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+maskambignuc \- Masks all ambiguity characters in nucleotide sequences with N
+.SH "SYNOPSIS"
+.HP 13
+\fBmaskambignuc\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP 13
+\fBmaskambignuc\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskambignuc\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskambignuc is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,59 @@
+.\" Title: MASKAMBIGPROT
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "MASKAMBIGPROT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+maskambigprot \- Masks all ambiguity characters in protein sequences with X
+.SH "SYNOPSIS"
+.HP 14
+\fBmaskambigprot\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP 14
+\fBmaskambigprot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskambigprot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskambigprot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MASKFEAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MASKFEAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MASKFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-maskfeat \- Mask off features of a sequence.
+maskfeat \- Write a sequence with masked features
.SH "SYNOPSIS"
.HP 9
\fBmaskfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/maskseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/maskseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MASKSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MASKSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MASKSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-maskseq \- Mask off regions of a sequence.
+maskseq \- Write a sequence with masked regions
.SH "SYNOPSIS"
.HP 8
\fBmaskseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/matcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/matcher.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/matcher.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MATCHER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MATCHER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-matcher \- Finds the best local alignments between two sequences
+matcher \- Waterman-Eggert local alignment of two sequences
.SH "SYNOPSIS"
.HP 8
\fBmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-alternatives\ \fR\fB\fIinteger\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/megamerger.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/megamerger.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/megamerger.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MEGAMERGER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MEGAMERGER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MEGAMERGER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-megamerger \- Merge two large overlapping nucleic acid sequences
+megamerger \- Merge two large overlapping DNA sequences
.SH "SYNOPSIS"
.HP 11
\fBmegamerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-prefer\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/merger.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/merger.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/merger.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: MERGER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MERGER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MERGER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/msbar.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/msbar.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/msbar.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MSBAR
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MSBAR" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MSBAR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-msbar \- Mutate sequence beyond all recognition
+msbar \- Mutate a sequence
.SH "SYNOPSIS"
.HP 6
\fBmsbar\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-othersequence\ \fR\fB\fIseqall\fR\fR \fB\-count\ \fR\fB\fIinteger\fR\fR \fB\-point\ \fR\fB\fIlist\fR\fR \fB\-block\ \fR\fB\fIlist\fR\fR \fB\-codon\ \fR\fB\fIlist\fR\fR \fB\-inframe\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MWCONTAM
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MWCONTAM" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MWCONTAM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-mwcontam \- Shows molwts that match across a set of files
+mwcontam \- Find weights common to multiple molecular weights files
.SH "SYNOPSIS"
.HP 9
\fBmwcontam\fR \fB\-files\ \fR\fB\fIfilelist\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: MWFILTER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "MWFILTER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "MWFILTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-mwfilter \- Filter noisy molwts from mass spec output
+mwfilter \- Filter noisy data from molecular weights file
.SH "SYNOPSIS"
.HP 9
\fBmwfilter\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR [\fB\-showdel\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/needle.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/needle.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/needle.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NEEDLE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NEEDLE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NEEDLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-needle \- Needleman-Wunsch global alignment.
+needle \- Needleman-Wunsch global alignment of two sequences
.SH "SYNOPSIS"
.HP 7
\fBneedle\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/newcoils.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcoils.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/newcoils.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: NEWCOILS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NEWCOILS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCOILS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NEWCPGREPORT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NEWCPGREPORT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCPGREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-newcpgreport \- Report CpG rich areas
+newcpgreport \- Identify CpG islands in nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 13
\fBnewcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-shift\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NEWCPGSEEK
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NEWCPGSEEK" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCPGSEEK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-newcpgseek \- Reports CpG rich regions
+newcpgseek \- Identify and report CpG-rich regions in nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 11
\fBnewcpgseek\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/newseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/newseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NEWSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NEWSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NEWSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-newseq \- Type in a short new sequence.
+newseq \- Create a sequence file from a typed-in sequence
.SH "SYNOPSIS"
.HP 7
\fBnewseq\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-description\ \fR\fB\fIstring\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/nohtml.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nohtml.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/nohtml.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,57 @@
+.\" Title: NOHTML
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "NOHTML" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+nohtml \- Remove mark-up (e.g. HTML tags) from an ASCII text file
+.SH "SYNOPSIS"
+.HP 7
+\fBnohtml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 7
+\fBnohtml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnohtml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nohtml is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/noreturn.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/noreturn.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/noreturn.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NORETURN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NORETURN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NORETURN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-noreturn \- Removes carriage return from ASCII files
+noreturn \- Remove carriage return from ASCII files
.SH "SYNOPSIS"
.HP 9
\fBnoreturn\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-system\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/nospace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nospace.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/nospace.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,57 @@
+.\" Title: NOSPACE
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "NOSPACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+nospace \- Remove all whitespace from an ASCII text file
+.SH "SYNOPSIS"
+.HP 8
+\fBnospace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 8
+\fBnospace\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnospace\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nospace is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/notab.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/notab.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/notab.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,57 @@
+.\" Title: NOTAB
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "NOTAB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+notab \- Replace tabs with spaces in an ASCII text file
+.SH "SYNOPSIS"
+.HP 6
+\fBnotab\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 6
+\fBnotab\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnotab\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+notab is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/notseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/notseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/notseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NOTSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NOTSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NOTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-notseq \- Exclude a set of sequences and write out the remaining ones
+notseq \- Write to file a subset of an input stream of sequences
.SH "SYNOPSIS"
.HP 7
\fBnotseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-junkoutseq\ \fR\fB\fIseqoutall\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/nthseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nthseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/nthseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: NTHSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "NTHSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "NTHSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-nthseq \- Writes one sequence from a multiple set of sequences
+nthseq \- Write to file a single sequence from an input stream of sequences
.SH "SYNOPSIS"
.HP 7
\fBnthseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/octanol.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/octanol.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/octanol.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: OCTANOL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "OCTANOL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "OCTANOL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-octanol \- Displays protein hydropathy
+octanol \- Draw a White-Wimley protein hydropathy plot
.SH "SYNOPSIS"
.HP 8
\fBoctanol\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-width\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-octanolplot\ \fR\fB\fIboolean\fR\fR] [\fB\-interfaceplot\ \fR\fB\fIboolean\fR\fR] [\fB\-differenceplot\ \fR\fB\fIboolean\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: ODDCOMP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ODDCOMP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ODDCOMP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-oddcomp \- Find protein sequence regions with a biased composition
+oddcomp \- Identify proteins with specified sequence word composition
.SH "SYNOPSIS"
.HP 8
\fBoddcomp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-fullwindow\ \fR\fB\fItoggle\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: ORIGSPLITTER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ORIGSPLITTER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ORIGSPLITTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/origunion.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/origunion.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/origunion.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: ORIGUNION
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "ORIGUNION" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "ORIGUNION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/palindrome.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/palindrome.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/palindrome.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PALINDROME
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PALINDROME" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PALINDROME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-palindrome \- Looks for inverted repeats in a nucleotide sequence
+palindrome \- Finds inverted repeats in nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 11
\fBpalindrome\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minpallen\ \fR\fB\fIinteger\fR\fR \fB\-maxpallen\ \fR\fB\fIinteger\fR\fR \fB\-gaplimit\ \fR\fB\fIinteger\fR\fR \fB\-nummismatches\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: PASTESEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PASTESEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PASTESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PATMATDB
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PATMATDB" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-patmatdb \- Search a protein sequence with a motif
+patmatdb \- Searches protein sequences with a sequence motif
.SH "SYNOPSIS"
.HP 9
\fBpatmatdb\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-motif\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PATMATMOTIFS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PATMATMOTIFS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATMOTIFS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-patmatmotifs \- Search a PROSITE motif database with a protein sequence
+patmatmotifs \- Scan a protein sequence with motifs from the PROSITE database
.SH "SYNOPSIS"
.HP 13
\fBpatmatmotifs\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-prune\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/patmattest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmattest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/patmattest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: PATMATTEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PATMATTEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: PEPCOIL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPCOIL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPCOIL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepcoil \- Predicts coiled coil regions
+pepcoil \- Predicts coiled coil regions in protein sequences
.SH "SYNOPSIS"
.HP 8
-\fBpepcoil\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-coil\ \fR\fB\fIboolean\fR\fR \fB\-frame\ \fR\fB\fIboolean\fR\fR \fB\-other\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+\fBpepcoil\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-coil\ \fR\fB\fIboolean\fR\fR \fB\-frame\ \fR\fB\fIboolean\fR\fR \fB\-other\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
.HP 8
\fBpepcoil\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -47,10 +47,10 @@
.PP
\fB\-other\fR \fIboolean\fR
.RS 4
-Default value: Y
+Default value: N
.RE
.PP
-\fB\-outfile\fR \fIoutfile\fR
+\fB\-outfile\fR \fIreport\fR
.RS 4
.RE
.SH "BUGS"
Modified: trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PEPINFO
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPINFO" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPINFO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepinfo \- Plots simple amino acid properties in parallel
+pepinfo \- Plot amino acid properties of a protein sequence in parallel.
.SH "SYNOPSIS"
.HP 8
\fBpepinfo\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-aaproperties\ \fR\fB\fIdatafile\fR\fR] [\fB\-aahydropathy\ \fR\fB\fIdatafile\fR\fR] [\fB\-hwindow\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-generalplot\ \fR\fB\fIboolean\fR\fR \fB\-hydropathyplot\ \fR\fB\fIboolean\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pepnet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepnet.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepnet.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PEPNET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPNET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPNET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepnet \- Displays proteins as a helical net
+pepnet \- Draw a helical net for a protein sequence
.SH "SYNOPSIS"
.HP 7
\fBpepnet\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pepstats.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepstats.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepstats.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,20 +1,20 @@
.\" Title: PEPSTATS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPSTATS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPSTATS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepstats \- Protein statistics
+pepstats \- Calculates statistics of protein properties
.SH "SYNOPSIS"
.HP 9
-\fBpepstats\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-termini\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+\fBpepstats\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-termini\ \fR\fB\fIboolean\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP 9
\fBpepstats\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -30,14 +30,24 @@
.PP
\fB\-aadata\fR \fIdatafile\fR
.RS 4
-Molecular weight data for amino acids Default value: Eamino\&.dat
+Amino acid properties Default value: Eamino\&.dat
.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
.SS "Advanced section"
.PP
\fB\-termini\fR \fIboolean\fR
.RS 4
Default value: Y
.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PEPWHEEL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPWHEEL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWHEEL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepwheel \- Shows protein sequences as helices
+pepwheel \- Draw a helical wheel diagram for a protein sequence
.SH "SYNOPSIS"
.HP 9
\fBpepwheel\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-wheel\ \fR\fB\fIboolean\fR\fR [\fB\-steps\ \fR\fB\fIinteger\fR\fR] [\fB\-turns\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PEPWINDOW
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPWINDOW" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWINDOW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepwindow \- Displays protein hydropathy
+pepwindow \- Draw a Kyte-Doolittle hydropathy plot for a protein sequence
.SH "SYNOPSIS"
.HP 10
\fBpepwindow\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PEPWINDOWALL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PEPWINDOWALL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWINDOWALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pepwindowall \- Displays protein hydropathy of a set of sequences
+pepwindowall \- Draw Kyte-Doolittle hydropathy plot for a protein alignment
.SH "SYNOPSIS"
.HP 13
\fBpepwindowall\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/plotcon.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/plotcon.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/plotcon.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PLOTCON
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PLOTCON" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PLOTCON" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-plotcon \- Plot quality of conservation of a sequence alignment
+plotcon \- Plot conservation of a sequence alignment
.SH "SYNOPSIS"
.HP 8
\fBplotcon\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-scorefile\ \fR\fB\fImatrix\fR\fR] \fB\-winsize\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/plotorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/plotorf.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/plotorf.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PLOTORF
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PLOTORF" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PLOTORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-plotorf \- Plot potential open reading frames
+plotorf \- Plot potential open reading frames in a nucleotide sequence
.SH "SYNOPSIS"
.HP 8
\fBplotorf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-start\ \fR\fB\fIstring\fR\fR \fB\-stop\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/polydot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/polydot.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/polydot.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: POLYDOT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "POLYDOT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "POLYDOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-polydot \- Displays all-against-all dotplots of a set of sequences
+polydot \- Draw dotplots for all-against-all comparison of a sequence set
.SH "SYNOPSIS"
.HP 8
\fBpolydot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] [\fB\-dumpfeat\ \fR\fB\fItoggle\fR\fR] \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/preg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/preg.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/preg.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PREG
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PREG" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PREG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-preg \- Regular expression search of a protein sequence
+preg \- Regular expression search of protein sequence(s)
.SH "SYNOPSIS"
.HP 5
\fBpreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PRETTYPLOT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRETTYPLOT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRETTYPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-prettyplot \- Displays aligned sequences, with colouring and boxing
+prettyplot \- Draw a sequence alignment with pretty formatting
.SH "SYNOPSIS"
.HP 11
\fBprettyplot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-resbreak\ \fR\fB\fIinteger\fR\fR] [\fB\-ccolours\ \fR\fB\fIboolean\fR\fR] [\fB\-cidentity\ \fR\fB\fIstring\fR\fR] [\fB\-csimilarity\ \fR\fB\fIstring\fR\fR] [\fB\-cother\ \fR\fB\fIstring\fR\fR] [\fB\-docolour\ \fR\fB\fIboolean\fR\fR] [\fB\-shade\ \fR\fB\fIstring\fR\fR] [\fB\-pair\ \fR\fB\fIarray\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-box\ \fR\fB\fIboolean\fR\fR] [\fB\-boxcol\ \fR\fB\fIboolean\fR\fR] [\fB\-boxcolval\ \fR\fB\fIstring\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-maxnamelen\ \fR\fB\fIinteger\fR\fR] [\fB\-number\ \fR\fB\fIboolean\fR\fR] [\fB\-listoptions\ \fR\fB\fIboolean\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] [\fB\-collision\ \fR\fB\fIboolean\fR\fR] [\fB\-alternative\ \fR\fB\fIlist\fR\fR] [\fB\-showscore\ \fR\fB\fIinteger\fR\fR] [\fB\-portrait\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PRETTYSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRETTYSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRETTYSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-prettyseq \- Output sequence with translated ranges
+prettyseq \- Write a nucleotide sequence and its translation to file
.SH "SYNOPSIS"
.HP 10
\fBprettyseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-range\ \fR\fB\fIrange\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prima.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prima.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prima.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: PRIMA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRIMA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/primers.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/primers.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/primers.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: PRIMERS
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRIMERS" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMERS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/primersearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/primersearch.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/primersearch.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PRIMERSEARCH
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRIMERSEARCH" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMERSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-primersearch \- Searches DNA sequences for matches with primer pairs
+primersearch \- Search DNA sequences for matches with primer pairs
.SH "SYNOPSIS"
.HP 13
\fBprimersearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mismatchpercent\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/printsextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/printsextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/printsextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PRINTSEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PRINTSEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PRINTSEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-printsextract \- Extract data from PRINTS
+printsextract \- Extract data from PRINTS database for use by pscan
.SH "SYNOPSIS"
.HP 14
\fBprintsextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/profit.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/profit.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/profit.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PROFIT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PROFIT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PROFIT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-profit \- Scan a sequence or database with a matrix or profile
+profit \- Scan one or more sequences with a simple frequency matrix
.SH "SYNOPSIS"
.HP 7
\fBprofit\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prophecy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prophecy.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prophecy.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PROPHECY
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PROPHECY" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PROPHECY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-prophecy \- Creates matrices/profiles from multiple alignments
+prophecy \- Create frequency matrix or profile from a multiple alignment
.SH "SYNOPSIS"
.HP 9
\fBprophecy\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-open\ \fR\fB\fIfloat\fR\fR \fB\-extension\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prophet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prophet.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prophet.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PROPHET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PROPHET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PROPHET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-prophet \- Gapped alignment for profiles
+prophet \- Scan one or more sequences with a Gribskov or Henikoff profile
.SH "SYNOPSIS"
.HP 8
\fBprophet\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/prosextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prosextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/prosextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PROSEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PROSEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PROSEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-prosextract \- Build the PROSITE motif database for use by patmatmotifs
+prosextract \- Processes the PROSITE motif database for use by patmatmotifs
.SH "SYNOPSIS"
.HP 12
\fBprosextract\fR \fB\-prositedir\ \fR\fB\fIdirectory\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/pscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pscan.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/pscan.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PSCAN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PSCAN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-pscan \- Scans proteins using PRINTS
+pscan \- Scans protein sequence(s) with fingerprints from the PRINTS database
.SH "SYNOPSIS"
.HP 6
\fBpscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-emin\ \fR\fB\fIinteger\fR\fR \fB\-emax\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/psiphi.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/psiphi.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/psiphi.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: PSIPHI
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "PSIPHI" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "PSIPHI" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-psiphi \- Phi and psi torsion angles from protein coordinates
+psiphi \- Calculates phi and psi torsion angles from protein coordinates
.SH "SYNOPSIS"
.HP 7
\fBpsiphi\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-chainnumber\ \fR\fB\fIinteger\fR\fR \fB\-startresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-finishresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: REBASEEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "REBASEEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "REBASEEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-rebaseextract \- Extract data from REBASE
+rebaseextract \- Process the REBASE database for use by restriction enzyme applications
.SH "SYNOPSIS"
.HP 14
\fBrebaseextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-protofile\ \fR\fB\fIinfile\fR\fR [\fB\-equivalences\ \fR\fB\fIboolean\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/recoder.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/recoder.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/recoder.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: RECODER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "RECODER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "RECODER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-recoder \- Remove restriction sites but maintain same translation
+recoder \- Find restriction sites to remove (mutate) with no translation change
.SH "SYNOPSIS"
.HP 8
\fBrecoder\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/redata.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/redata.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/redata.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: REDATA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "REDATA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "REDATA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-redata \- Search REBASE for enzyme name, references, suppliers etc.
+redata \- Retrieve information from REBASE restriction enzyme database
.SH "SYNOPSIS"
.HP 7
\fBredata\fR \fB\-enzyme\ \fR\fB\fIstring\fR\fR \fB\-isoschizomers\ \fR\fB\fIboolean\fR\fR \fB\-references\ \fR\fB\fIboolean\fR\fR \fB\-suppliers\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/remap.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/remap.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/remap.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: REMAP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "REMAP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "REMAP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-remap \- Display sequence with restriction sites, translation etc.
+remap \- Display restriction enzyme binding sites in a nucleotide sequence
.SH "SYNOPSIS"
.HP 6
\fBremap\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR [\fB\-mincuts\ \fR\fB\fIinteger\fR\fR] [\fB\-maxcuts\ \fR\fB\fIinteger\fR\fR] [\fB\-single\ \fR\fB\fIboolean\fR\fR] [\fB\-blunt\ \fR\fB\fIboolean\fR\fR] [\fB\-sticky\ \fR\fB\fIboolean\fR\fR] [\fB\-ambiguity\ \fR\fB\fIboolean\fR\fR] [\fB\-plasmid\ \fR\fB\fIboolean\fR\fR] [\fB\-commercial\ \fR\fB\fIboolean\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-frame\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-cutlist\ \fR\fB\fIboolean\fR\fR] [\fB\-flatreformat\ \fR\fB\fIboolean\fR\fR] [\fB\-limit\ \fR\fB\fIboolean\fR\fR] \fB\-translation\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/restover.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/restover.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/restover.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: RESTOVER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "RESTOVER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "RESTOVER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-restover \- Find restriction enzymes producing specific overhang
+restover \- Find restriction enzymes producing a specific overhang
.SH "SYNOPSIS"
.HP 9
\fBrestover\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-seqcomp\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-threeprime\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/restrict.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/restrict.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/restrict.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: RESTRICT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "RESTRICT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "RESTRICT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-restrict \- Finds restriction enzyme cleavage sites
+restrict \- Report restriction enzyme cleavage sites in a nucleotide sequence
.SH "SYNOPSIS"
.HP 9
\fBrestrict\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-solofragment\ \fR\fB\fIboolean\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/revseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/revseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/revseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: REVSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "REVSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "REVSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-revseq \- Reverse and complement a sequence
+revseq \- Reverse and complement a nucleotide sequence
.SH "SYNOPSIS"
.HP 7
\fBrevseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/seealso.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seealso.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seealso.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SEEALSO
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEEALSO" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEEALSO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-seealso \- Finds programs sharing group names
+seealso \- Finds programs with similar function to a specified program
.SH "SYNOPSIS"
.HP 8
\fBseealso\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] \fB\-colon\ \fR\fB\fIboolean\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQINFO
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQINFO" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQINFO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SEQMATCHALL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQMATCHALL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQMATCHALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-seqmatchall \- All-against-all comparison of a set of sequences
+seqmatchall \- All-against-all word comparison of a sequence set
.SH "SYNOPSIS"
.HP 12
\fBseqmatchall\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/seqret.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqret.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqret.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -35,6 +35,7 @@
.PP
\fB\-firstonly\fR \fIboolean\fR
.RS 4
+Default value: N
.RE
.SS "Output section"
.PP
Modified: trunk/packages/emboss/trunk/debian/manpages/seqretall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretall.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretall.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRETALL
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETALL" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRETALLFEAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETALLFEAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETALLFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/seqretset.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretset.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretset.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRETSET
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETSET" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRETSINGLE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETSINGLE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSINGLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SEQRETSPLIT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETSPLIT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSPLIT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-seqretsplit \- Reads and writes (returns) sequences in individual files
+seqretsplit \- Reads sequences and writes them to individual files
.SH "SYNOPSIS"
.HP 12
\fBseqretsplit\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SEQRETTYPE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SEQRETTYPE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETTYPE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/showalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showalign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/showalign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SHOWALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHOWALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-showalign \- Displays a multiple sequence alignment
+showalign \- Display a multiple sequence alignment in pretty format
.SH "SYNOPSIS"
.HP 10
\fBshowalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] [\fB\-bottom\ \fR\fB\fIboolean\fR\fR] [\fB\-show\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-similarcase\ \fR\fB\fIboolean\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-setcase\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/showdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showdb.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/showdb.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SHOWDB
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHOWDB" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-showdb \- Displays information on the currently available databases
+showdb \- Displays information on configured databases
.SH "SYNOPSIS"
.HP 7
\fBshowdb\fR [\fB\-database\ \fR\fB\fIstring\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-protein\ \fR\fB\fIboolean\fR\fR] [\fB\-nucleic\ \fR\fB\fIboolean\fR\fR] [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-methods\ \fR\fB\fIboolean\fR\fR] [\fB\-fields\ \fR\fB\fIboolean\fR\fR] [\fB\-defined\ \fR\fB\fIboolean\fR\fR] [\fB\-release\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fItoggle\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-query\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-comment\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/showfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showfeat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/showfeat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SHOWFEAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHOWFEAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-showfeat \- Show features of a sequence.
+showfeat \- Display features of a sequence in pretty format
.SH "SYNOPSIS"
.HP 9
\fBshowfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-matchsource\ \fR\fB\fIstring\fR\fR] [\fB\-matchtype\ \fR\fB\fIstring\fR\fR] [\fB\-matchtag\ \fR\fB\fIstring\fR\fR] [\fB\-matchvalue\ \fR\fB\fIstring\fR\fR] [\fB\-sort\ \fR\fB\fIlist\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-scale\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-collapse\ \fR\fB\fIboolean\fR\fR \fB\-forward\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-unknown\ \fR\fB\fIboolean\fR\fR \fB\-strand\ \fR\fB\fIboolean\fR\fR \fB\-source\ \fR\fB\fIboolean\fR\fR \fB\-position\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-tags\ \fR\fB\fIboolean\fR\fR \fB\-values\ \fR\fB\fIboolean\fR\fR \fB\-stricttags\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/showorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showorf.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/showorf.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SHOWORF
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHOWORF" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-showorf \- Pretty output of DNA translations
+showorf \- Display a nucleotide sequence and translation in pretty format
.SH "SYNOPSIS"
.HP 8
\fBshoworf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-frames\ \fR\fB\fIlist\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/showseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/showseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SHOWSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHOWSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-showseq \- Display a sequence with features, translation etc..
+showseq \- Displays sequences with features in pretty format
.SH "SYNOPSIS"
.HP 8
\fBshowseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-translate\ \fR\fB\fIrange\fR\fR] [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-enzymes\ \fR\fB\fIstring\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-matchsource\ \fR\fB\fIstring\fR\fR] [\fB\-matchtype\ \fR\fB\fIstring\fR\fR] [\fB\-matchsense\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-matchtag\ \fR\fB\fIstring\fR\fR] [\fB\-matchvalue\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\fR\fR] \fB\-flatreformat\ \fR\fB\fIboolean\fR\fR \fB\-mincuts\ \fR\fB\fIinteger\fR\fR \fB\-maxcuts\ \fR\fB\fIinteger\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SHUFFLESEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SHUFFLESEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SHUFFLESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SIGCLEAVE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SIGCLEAVE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SIGCLEAVE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-sigcleave \- Reports protein signal cleavage sites
+sigcleave \- Reports on signal cleavage sites in a protein sequence
.SH "SYNOPSIS"
.HP 10
\fBsigcleave\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minweight\ \fR\fB\fIfloat\fR\fR [\fB\-prokaryote\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/silent.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/silent.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/silent.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SILENT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SILENT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SILENT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-silent \- Silent mutation restriction enzyme scan
+silent \- Find restriction sites to insert (mutate) with no translation change
.SH "SYNOPSIS"
.HP 7
\fBsilent\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-allmut\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/sirna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sirna.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/sirna.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SIRNA
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SIRNA" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SIRNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/sixpack.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sixpack.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/sixpack.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SIXPACK
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SIXPACK" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SIXPACK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Added: trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,67 @@
+.\" Title: SIZESEQ
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "SIZESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+sizeseq \- Sort sequences by size
+.SH "SYNOPSIS"
+.HP 8
+\fBsizeseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-descending\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP 8
+\fBsizeseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsizeseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Sequence feature information will be retained if this option is set\&.
+.RE
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-descending\fR \fIboolean\fR
+.RS 4
+By default the shortest sequence is given first\&. Default value: N
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sizeseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Added: trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,105 @@
+.\" Title: SKIPREDUNDANT
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "SKIPREDUNDANT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+skipredundant \- Remove redundant sequences from an input set
+.SH "SYNOPSIS"
+.HP 14
+\fBskipredundant\fR \fB\-feature\ \fR\fB\fItoggle\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-minthreshold\ \fR\fB\fIfloat\fR\fR \fB\-maxthreshold\ \fR\fB\fIfloat\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-keepredundant\ \fR\fB\fItoggle\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-redundantoutseq\ \fR\fB\fIseqoutall\fR\fR
+.HP 14
+\fBskipredundant\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBskipredundant\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fItoggle\fR
+.RS 4
+Sequence feature information will be retained if this option is set\&.
+.RE
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \'EBLOSUM62\' (for proteins) or the file \'EDNAFULL\' (for nucleic sequences)\&. These files are found in the \'data\' directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+This option specifies whether to remove redundancy at a single threshold percentage sequence similarity or remove redundancy outside a range of acceptable threshold percentage similarity\&. All permutations of pair\-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0
+.RE
+.PP
+\fB\-minthreshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold (lower limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0
+.RE
+.PP
+\fB\-maxthreshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold (upper limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0
+.RE
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.SS "Advanced section"
+.PP
+\fB\-keepredundant\fR \fItoggle\fR
+.RS 4
+This option specifies whether to retain redundant sequences\&. If this option is set a file of redundant sequences is written\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-redundantoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+skipredundant is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/skipseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/skipseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/skipseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: SKIPSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SKIPSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SKIPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/splitter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/splitter.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/splitter.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SPLITTER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SPLITTER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SPLITTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-splitter \- Split a sequence into (overlapping) smaller sequences
+splitter \- Split sequence(s) into smaller sequences
.SH "SYNOPSIS"
.HP 9
\fBsplitter\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] [\fB\-source\ \fR\fB\fIboolean\fR\fR] [\fB\-multifile\ \fR\fB\fIboolean\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/stretcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/stretcher.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/stretcher.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: STRETCHER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "STRETCHER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "STRETCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-stretcher \- Finds the best global alignment between two sequences
+stretcher \- Needleman-Wunsch rapid global alignment of two sequences
.SH "SYNOPSIS"
.HP 10
\fBstretcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/stssearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/stssearch.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/stssearch.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: STSSEARCH
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "STSSEARCH" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "STSSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SUPERMATCHER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SUPERMATCHER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SUPERMATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-supermatcher \- Match large sequences against one or more other sequences
+supermatcher \- Calculate approximate local pair-wise alignments of larger sequences
.SH "SYNOPSIS"
.HP 13
\fBsupermatcher\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/syco.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/syco.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/syco.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: SYCO
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "SYCO" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "SYCO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-syco \- Synonymous codon usage Gribskov statistic plot
+syco \- Draw synonymous codon usage statictic plot for a nucleotide sequence
.SH "SYNOPSIS"
.HP 5
\fBsyco\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-uncommon\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/tcode.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tcode.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tcode.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TCODE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TCODE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TCODE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tcode \- Fickett TESTCODE statistic to identify protein-coding DNA
+tcode \- Identify protein-coding regions using Fickett TESTCODE statistic
.SH "SYNOPSIS"
.HP 6
\fBtcode\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/testplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/testplot.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/testplot.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: TESTPLOT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TESTPLOT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TESTPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/textsearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/textsearch.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/textsearch.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TEXTSEARCH
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TEXTSEARCH" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TEXTSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-textsearch \- Search sequence documentation. Slow, use SRS and Entrez!
+textsearch \- Search the textual description of sequence(s)
.SH "SYNOPSIS"
.HP 11
\fBtextsearch\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIstring\fR\fR [\fB\-casesensitive\ \fR\fB\fIboolean\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/tfextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfextract.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tfextract.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TFEXTRACT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TFEXTRACT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TFEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tfextract \- Extract data from TRANSFAC
+tfextract \- Process TRANSFAC transcription factor database for use by tfscan
.SH "SYNOPSIS"
.HP 10
\fBtfextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/tfm.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfm.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tfm.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TFM
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TFM" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TFM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tfm \- Displays a program's help documentation manual
+tfm \- Displays full documentation for an application
.SH "SYNOPSIS"
.HP 4
\fBtfm\fR \fB\-program\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-more\ \fR\fB\fIboolean\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/tfscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfscan.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tfscan.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TFSCAN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TFSCAN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TFSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tfscan \- Scans DNA sequences for transcription factors
+tfscan \- Identify transcription factor binding sites in DNA sequences
.SH "SYNOPSIS"
.HP 7
\fBtfscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-custom\ \fR\fB\fIdatafile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/tmap.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tmap.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tmap.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TMAP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TMAP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TMAP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tmap \- Displays membrane spanning regions
+tmap \- Predict and plot transmembrane segments in protein sequences
.SH "SYNOPSIS"
.HP 5
\fBtmap\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/tranalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tranalign.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/tranalign.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TRANALIGN
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TRANALIGN" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TRANALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-tranalign \- Align nucleic coding regions given the aligned proteins
+tranalign \- Generate an aligment of nucleic coding regions from aligned proteins
.SH "SYNOPSIS"
.HP 10
\fBtranalign\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/transeq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/transeq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/transeq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: TRANSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TRANSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TRANSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: TREETYPEDISPLAY
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TREETYPEDISPLAY" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TREETYPEDISPLAY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/trimest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimest.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/trimest.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TRIMEST
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TRIMEST" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TRIMEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-trimest \- Trim poly-A tails off EST sequences
+trimest \- Remove poly-A tails from nucleotide sequences
.SH "SYNOPSIS"
.HP 8
\fBtrimest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatches\ \fR\fB\fIinteger\fR\fR] [\fB\-reverse\ \fR\fB\fIboolean\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-fiveprime\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/trimseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimseq.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/trimseq.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TRIMSEQ
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TRIMSEQ" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TRIMSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-trimseq \- Trim ambiguous bits off the ends of sequences
+trimseq \- Remove unwanted characters from start and end of sequence(s)
.SH "SYNOPSIS"
.HP 8
\fBtrimseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-percent\ \fR\fB\fIfloat\fR\fR] [\fB\-strict\ \fR\fB\fIboolean\fR\fR] [\fB\-star\ \fR\fB\fIboolean\fR\fR] \fB\-left\ \fR\fB\fIboolean\fR\fR \fB\-right\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Added: trunk/packages/emboss/trunk/debian/manpages/trimspace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimspace.1e (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/trimspace.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -0,0 +1,57 @@
+.\" Title: TRIMSPACE
+.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 07/16/2008
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 6.0.0
+.\"
+.TH "TRIMSPACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+trimspace \- Remove extra whitespace from an ASCII text file
+.SH "SYNOPSIS"
+.HP 10
+\fBtrimspace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 10
+\fBtrimspace\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtrimspace\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+trimspace is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\&.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian-Med Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Modified: trunk/packages/emboss/trunk/debian/manpages/twofeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/twofeat.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/twofeat.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: TWOFEAT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "TWOFEAT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "TWOFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-twofeat \- Finds neighbouring pairs of features in sequences
+twofeat \- Finds neighbouring pairs of features in sequence(s)
.SH "SYNOPSIS"
.HP 8
\fBtwofeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-asource\ \fR\fB\fIstring\fR\fR] \fB\-atype\ \fR\fB\fIstring\fR\fR [\fB\-asense\ \fR\fB\fIlist\fR\fR] [\fB\-aminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-amaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-atag\ \fR\fB\fIstring\fR\fR] [\fB\-avalue\ \fR\fB\fIstring\fR\fR] [\fB\-bsource\ \fR\fB\fIstring\fR\fR] \fB\-btype\ \fR\fB\fIstring\fR\fR [\fB\-bsense\ \fR\fB\fIlist\fR\fR] [\fB\-bminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-bmaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-btag\ \fR\fB\fIstring\fR\fR] [\fB\-bvalue\ \fR\fB\fIstring\fR\fR] [\fB\-overlap\ \fR\fB\fIlist\fR\fR] \fB\-minrange\ \fR\fB\fIinteger\fR\fR \fB\-maxrange\ \fR\fB\fIinteger\fR\fR [\fB\-rangetype\ \fR\fB\fIlist\fR\fR] [\fB\-sense\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-twoout\ \fR\fB\fItoggle\fR\fR] \fB\-typeout\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/union.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/union.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/union.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: UNION
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "UNION" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "UNION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-union \- Reads sequence fragments and builds one sequence
+union \- Concatenate multiple sequences into a single sequence
.SH "SYNOPSIS"
.HP 6
\fBunion\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-source\ \fR\fB\fIboolean\fR\fR \fB\-findoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-overlapfile\ \fR\fB\fIoutfile\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: VECTORSTRIP
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "VECTORSTRIP" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "VECTORSTRIP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-vectorstrip \- Strips out DNA between a pair of vector sequences
+vectorstrip \- Removes vectors from the ends of nucleotide sequence(s)
.SH "SYNOPSIS"
.HP 12
\fBvectorstrip\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-vectorfile\ \fR\fB\fItoggle\fR\fR \fB\-vectorsfile\ \fR\fB\fIinfile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR \fB\-besthits\ \fR\fB\fIboolean\fR\fR \fB\-linkera\ \fR\fB\fIstring\fR\fR \fB\-linkerb\ \fR\fB\fIstring\fR\fR [\fB\-allsequences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/water.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/water.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/water.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WATER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WATER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WATER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-water \- Smith-Waterman local alignment.
+water \- Smith-Waterman local alignment of sequences
.SH "SYNOPSIS"
.HP 6
\fBwater\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/whichdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/whichdb.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/whichdb.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WHICHDB
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WHICHDB" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WHICHDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-whichdb \- Search all databases for an entry
+whichdb \- Search all sequence databases for an entry and retrieve it
.SH "SYNOPSIS"
.HP 8
\fBwhichdb\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-get\ \fR\fB\fItoggle\fR\fR \fB\-showall\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/wobble.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wobble.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/wobble.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WOBBLE
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WOBBLE" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WOBBLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-wobble \- Wobble base plot
+wobble \- Plot third base position variability in a nucleotide sequence
.SH "SYNOPSIS"
.HP 7
\fBwobble\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-bases\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/wordcount.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordcount.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/wordcount.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WORDCOUNT
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WORDCOUNT" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WORDCOUNT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-wordcount \- Counts words of a specified size in a DNA sequence
+wordcount \- Count and extract unique words in DNA sequence(s)
.SH "SYNOPSIS"
.HP 10
\fBwordcount\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-mincount\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
@@ -20,7 +20,7 @@
.SH "DESCRIPTION"
.PP
\fBwordcount\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition " command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
@@ -31,7 +31,7 @@
.PP
\fB\-wordsize\fR \fIinteger\fR
.RS 4
-Default value: 4
+Default value: @($(acdprotein)? 2 : 4)
.RE
.SS "Additional section"
.PP
Modified: trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,11 +1,11 @@
.\" Title: WORDFINDER
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WORDFINDER" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WORDFINDER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WORDMATCH
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WORDMATCH" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WORDMATCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-wordmatch \- Finds all exact matches of a given size between 2 sequences
+wordmatch \- Finds regions of identity (exact matches) of two sequences
.SH "SYNOPSIS"
.HP 10
\fBwordmatch\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR
Modified: trunk/packages/emboss/trunk/debian/manpages/wossname.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wossname.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/wossname.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: WOSSNAME
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "WOSSNAME" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "WOSSNAME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-wossname \- Finds programs by keywords in their one-line documentation
+wossname \- Finds programs by keywords in their short description
.SH "SYNOPSIS"
.HP 9
\fBwossname\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-allmatch\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
Modified: trunk/packages/emboss/trunk/debian/manpages/yank.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/yank.1e 2008-07-16 04:10:38 UTC (rev 2238)
+++ trunk/packages/emboss/trunk/debian/manpages/yank.1e 2008-07-16 06:03:16 UTC (rev 2239)
@@ -1,17 +1,17 @@
.\" Title: YANK
.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/16/2008
+.\" Date: 07/16/2008
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 5.0.0
+.\" Source: EMBOSS 6.0.0
.\"
-.TH "YANK" "1e" "05/16/2008" "EMBOSS 5.0.0" "EMBOSS Manual for Debian"
+.TH "YANK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-yank \- Reads a sequence range, appends the full USA to a list file
+yank \- Add a sequence reference (a full USA) to a list file
.SH "SYNOPSIS"
.HP 5
\fByank\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-newfile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
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