[med-svn] r3639 - in trunk/packages/emboss/trunk/debian: . manpages

Wed Jul 15 13:10:25 UTC 2009

Author: plessy
Date: 2009-07-15 13:10:24 +0000 (Wed, 15 Jul 2009)
New Revision: 3639

Added:
   trunk/packages/emboss/trunk/debian/manpages/dbxreport.1e
   trunk/packages/emboss/trunk/debian/manpages/nthseqset.1e
   trunk/packages/emboss/trunk/debian/manpages/seqretsetall.1e
   trunk/packages/emboss/trunk/debian/manpages/showpep.1e
   trunk/packages/emboss/trunk/debian/manpages/splitsource.1e
Modified:
   trunk/packages/emboss/trunk/debian/acd2docbook.pl
   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/aligncopy.1e
   trunk/packages/emboss/trunk/debian/manpages/aligncopypair.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/consambig.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/density.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/featcopy.1e
   trunk/packages/emboss/trunk/debian/manpages/featreport.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/infobase.1e
   trunk/packages/emboss/trunk/debian/manpages/inforesidue.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/jaspextract.1e
   trunk/packages/emboss/trunk/debian/manpages/jaspscan.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/maskambignuc.1e
   trunk/packages/emboss/trunk/debian/manpages/maskambigprot.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/nohtml.1e
   trunk/packages/emboss/trunk/debian/manpages/noreturn.1e
   trunk/packages/emboss/trunk/debian/manpages/nospace.1e
   trunk/packages/emboss/trunk/debian/manpages/notab.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/sizeseq.1e
   trunk/packages/emboss/trunk/debian/manpages/skipredundant.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/trimspace.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:
Created and refreshed manpages for new upstream version.


Modified: trunk/packages/emboss/trunk/debian/acd2docbook.pl
===================================================================

--- trunk/packages/emboss/trunk/debian/acd2docbook.pl	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/acd2docbook.pl	2009-07-15 13:10:24 UTC (rev 3639)
@@ -60,10 +60,6 @@
 				</address>
 			</author>
 		</authorgroup>
-		<copyright>
-			<year>2007</year>
-			<holder>&dhusername;</holder>
-		</copyright>
 		<legalnotice>
 			<para>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.</para>
 		</legalnotice>
@@ -128,7 +124,7 @@
 	}
 
 	# Is there a Default value ?
-	my $default;
+	my $default = '';
 	$default = " Default value: $$parameter{default}" if $$parameter{default};
 
 	# Use entities when necessary:

Modified: trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/aaindexextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "AAINDEXEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "AAINDEXEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 aaindexextract \- Extract amino acid property data from AAINDEX
 .SH "SYNOPSIS"
-.HP 15
+.HP \w'\fBaaindexextract\fR\ 'u
 \fBaaindexextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
-.HP 15
+.HP \w'\fBaaindexextract\fR\ 'u
 \fBaaindexextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/abiview.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/abiview.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/abiview.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ABIVIEW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ABIVIEW" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 abiview \- Display the trace in an ABI sequencer file
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBabiview\fR\ 'u
 \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]
-.HP 8
+.HP \w'\fBabiview\fR\ 'u
 \fBabiview\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -81,11 +89,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdc.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdc.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDC" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdc \- Test an application ACD file
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBacdc\fR\ 'u
 \fBacdc\fR
-.HP 5
+.HP \w'\fBacdc\fR\ 'u
 \fBacdc\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,11 +41,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdlog.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdlog.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdlog.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDLOG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDLOG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdlog \- Test application ACD file processing and trace data structures
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBacdlog\fR\ 'u
 \fBacdlog\fR
-.HP 7
+.HP \w'\fBacdlog\fR\ 'u
 \fBacdlog\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,11 +41,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdpretty.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDPRETTY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDPRETTY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdpretty \- Correctly reformat an application ACD file
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBacdpretty\fR\ 'u
 \fBacdpretty\fR
-.HP 10
+.HP \w'\fBacdpretty\fR\ 'u
 \fBacdpretty\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,11 +41,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdtable.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdtable.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdtable.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDTABLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDTABLE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdtable \- Generate an HTML table of parameters from an application ACD file
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBacdtable\fR\ 'u
 \fBacdtable\fR
-.HP 9
+.HP \w'\fBacdtable\fR\ 'u
 \fBacdtable\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,11 +41,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdtrace.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDTRACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDTRACE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdtrace \- Trace processing of an application ACD file (for testing)
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBacdtrace\fR\ 'u
 \fBacdtrace\fR \fB\-program\ \fR\fB\fIstring\fR\fR
-.HP 9
+.HP \w'\fBacdtrace\fR\ 'u
 \fBacdtrace\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/acdvalid.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ACDVALID" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ACDVALID" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 acdvalid \- Validate an application ACD file
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBacdvalid\fR\ 'u
 \fBacdvalid\fR
-.HP 9
+.HP \w'\fBacdvalid\fR\ 'u
 \fBacdvalid\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,11 +41,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/ajbad.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajbad.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/ajbad.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "AJBAD" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "AJBAD" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 ajbad \- Test file for ACD parsing
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBajbad\fR\ 'u
 \fBajbad\fR \fB\-typea\ \fR\fB\fIstring\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-eco\ \fR\fB\fIcodon\fR\fR \fB\-typeb\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-a\ \fR\fB\fIinteger\fR\fR \fB\-b\ \fR\fB\fIinteger\fR\fR \fB\-c\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 6
+.HP \w'\fBajbad\fR\ 'u
 \fBajbad\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -81,11 +89,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/ajfeatest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "AJFEATEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "AJFEATEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 ajfeatest \- Reads and writes (returns) a sequence and its features
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBajfeatest\fR\ 'u
 \fBajfeatest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 10
+.HP \w'\fBajfeatest\fR\ 'u
 \fBajfeatest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/ajtest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/ajtest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/ajtest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "AJTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "AJTEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 ajtest \- Test file for ACD parsing
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBajtest\fR\ 'u
 \fBajtest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-outdir\ \fR\fB\fIoutdir\fR\fR
-.HP 7
+.HP \w'\fBajtest\fR\ 'u
 \fBajtest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/aligncopy.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ALIGNCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ALIGNCOPY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 aligncopy \- Reads and writes alignments
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBaligncopy\fR\ 'u
 \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
+.HP \w'\fBaligncopy\fR\ 'u
 \fBaligncopy\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/aligncopypair.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ALIGNCOPYPAIR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ALIGNCOPYPAIR" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 aligncopypair \- Reads and writes pairs from alignments
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBaligncopypair\fR\ 'u
 \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
+.HP \w'\fBaligncopypair\fR\ 'u
 \fBaligncopypair\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/antigenic.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/antigenic.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/antigenic.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ANTIGENIC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ANTIGENIC" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 antigenic \- Finds antigenic sites in proteins
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBantigenic\fR\ 'u
 \fBantigenic\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 10
+.HP \w'\fBantigenic\fR\ 'u
 \fBantigenic\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/backtranambig.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "BACKTRANAMBIG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "BACKTRANAMBIG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-backtranambig \- Back-translate a protein sequence to ambiguous nucleotide sequence
+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
-.HP 14
+.HP \w'\fBbacktranambig\fR\ 'u
+\fBbacktranambig\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBbacktranambig\fR\ 'u
 \fBbacktranambig\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -24,7 +32,7 @@
 .SH "OPTIONS"
 .SS "Input section"
 .PP
-\fB\-sequence\fR \fIsequence\fR
+\fB\-sequence\fR \fIseqall\fR
 .RS 4
 .RE
 .SS "Additional section"
@@ -34,7 +42,7 @@
 .RE
 .SS "Output section"
 .PP
-\fB\-outfile\fR \fIseqout\fR
+\fB\-outfile\fR \fIseqoutall\fR
 .RS 4
 .RE
 .SH "BUGS"
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/backtranseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "BACKTRANSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "BACKTRANSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-backtranseq \- Back-translate a protein sequence to a nucleotide 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
-.HP 12
+.HP \w'\fBbacktranseq\fR\ 'u
+\fBbacktranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-cfile\ \fR\fB\fIcodon\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBbacktranseq\fR\ 'u
 \fBbacktranseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -24,7 +32,7 @@
 .SH "OPTIONS"
 .SS "Input section"
 .PP
-\fB\-sequence\fR \fIsequence\fR
+\fB\-sequence\fR \fIseqall\fR
 .RS 4
 .RE
 .PP
@@ -34,7 +42,7 @@
 .RE
 .SS "Output section"
 .PP
-\fB\-outfile\fR \fIseqout\fR
+\fB\-outfile\fR \fIseqoutall\fR
 .RS 4
 .RE
 .SH "BUGS"
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/banana.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/banana.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/banana.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "BANANA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "BANANA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-banana \- Plot bending and curvature data for B-DNA
+banana \- Plot bending and curvature data for B\-DNA
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBbanana\fR\ 'u
 \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]
-.HP 7
+.HP \w'\fBbanana\fR\ 'u
 \fBbanana\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/biosed.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/biosed.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/biosed.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "BIOSED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "BIOSED" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 biosed \- Replace or delete sequence sections
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBbiosed\fR\ 'u
 \fBbiosed\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-target\ \fR\fB\fIstring\fR\fR \fB\-delete\ \fR\fB\fItoggle\fR\fR \fB\-replace\ \fR\fB\fIstring\fR\fR [\fB\-position\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 7
+.HP \w'\fBbiosed\fR\ 'u
 \fBbiosed\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -64,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/btwisted.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/btwisted.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/btwisted.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "BTWISTED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "BTWISTED" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-btwisted \- Calculate the twisting in a B-DNA sequence
+btwisted \- Calculate the twisting in a B\-DNA sequence
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBbtwisted\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBbtwisted\fR\ 'u
 \fBbtwisted\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -53,11 +61,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cai.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cai.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cai.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CAI" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CAI" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cai \- Calculate codon adaptation index
 .SH "SYNOPSIS"
-.HP 4
+.HP \w'\fBcai\fR\ 'u
 \fBcai\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 4
+.HP \w'\fBcai\fR\ 'u
 \fBcai\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/chaos.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/chaos.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/chaos.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CHAOS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CHAOS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 chaos \- Draw a chaos game representation plot for a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBchaos\fR\ 'u
 \fBchaos\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
-.HP 6
+.HP \w'\fBchaos\fR\ 'u
 \fBchaos\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/charge.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/charge.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/charge.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CHARGE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CHARGE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 charge \- Draw a protein charge plot
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBcharge\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBcharge\fR\ 'u
 \fBcharge\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/checktrans.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/checktrans.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/checktrans.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CHECKTRANS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CHECKTRANS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 checktrans \- Reports STOP codons and ORF statistics of a protein
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBchecktrans\fR\ 'u
 \fBchecktrans\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-orfml\ \fR\fB\fIinteger\fR\fR [\fB\-addlast\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
-.HP 11
+.HP \w'\fBchecktrans\fR\ 'u
 \fBchecktrans\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -65,11 +73,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/chips.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/chips.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/chips.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CHIPS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CHIPS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 chips \- Calculates Nc codon usage statistic
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBchips\fR\ 'u
 \fBchips\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-sum\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 6
+.HP \w'\fBchips\fR\ 'u
 \fBchips\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cirdna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cirdna.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cirdna.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CIRDNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CIRDNA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cirdna \- Draws circular maps of DNA constructs
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBcirdna\fR\ 'u
 \fBcirdna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-originangle\ \fR\fB\fIfloat\fR\fR] \fB\-posticks\ \fR\fB\fIselection\fR\fR \fB\-posblocks\ \fR\fB\fIselection\fR\fR [\fB\-intersymbol\ \fR\fB\fIboolean\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR
-.HP 7
+.HP \w'\fBcirdna\fR\ 'u
 \fBcirdna\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -140,11 +148,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/codcmp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/codcmp.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/codcmp.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CODCMP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CODCMP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 codcmp \- Codon usage table comparison
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBcodcmp\fR\ 'u
 \fBcodcmp\fR \fB\-first\ \fR\fB\fIcodon\fR\fR \fB\-second\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBcodcmp\fR\ 'u
 \fBcodcmp\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/codcopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/codcopy.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/codcopy.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CODCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CODCOPY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 codcopy \- Copy and reformat a codon usage table
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBcodcopy\fR\ 'u
 \fBcodcopy\fR \fB\-infile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutcodon\fR\fR
-.HP 8
+.HP \w'\fBcodcopy\fR\ 'u
 \fBcodcopy\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/coderet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/coderet.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/coderet.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CODERET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CODERET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 coderet \- Extract CDS, mRNA and translations from feature tables
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBcoderet\fR\ 'u
 \fBcoderet\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-cdsoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-mrnaoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-translationoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-restoutseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 8
+.HP \w'\fBcoderet\fR\ 'u
 \fBcoderet\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/complex.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/complex.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/complex.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "COMPLEX" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "COMPLEX" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 complex \- Find the linguistic complexity in nucleotide sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBcomplex\fR\ 'u
 \fBcomplex\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-lwin\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-jmin\ \fR\fB\fIinteger\fR\fR \fB\-jmax\ \fR\fB\fIinteger\fR\fR \fB\-omnia\ \fR\fB\fItoggle\fR\fR \fB\-sim\ \fR\fB\fIinteger\fR\fR \fB\-freq\ \fR\fB\fIboolean\fR\fR \fB\-print\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-ujtablefile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 8
+.HP \w'\fBcomplex\fR\ 'u
 \fBcomplex\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -93,11 +101,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/compseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/compseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/compseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "COMPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "COMPSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 compseq \- Calculate the composition of unique words in sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBcompseq\fR\ 'u
 \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]
-.HP 8
+.HP \w'\fBcompseq\fR\ 'u
 \fBcompseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -36,7 +44,7 @@
 .PP
 \fB\-word\fR \fIinteger\fR
 .RS 4
-This is the size of word (n\-mer) to count\&. Thus if you want to count codon frequencies, you should enter 3 here\&. Default value: 2
+This is the size of word (n\-mer) to count\&. Thus if you want to count codon frequencies for a nucleotide sequence, you should enter 3 here\&. Default value: 2
 .RE
 .SS "Additional section"
 .PP
@@ -81,11 +89,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cons.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cons.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cons.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CONS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CONS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cons \- Create a consensus sequence from a multiple alignment
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBcons\fR\ 'u
 \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]
-.HP 5
+.HP \w'\fBcons\fR\ 'u
 \fBcons\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/consambig.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/consambig.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/consambig.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CONSAMBIG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CONSAMBIG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 consambig \- Create an ambiguous consensus sequence from a multiple alignment
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBconsambig\fR\ 'u
 \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
+.HP \w'\fBconsambig\fR\ 'u
 \fBconsambig\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/corbatest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/corbatest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/corbatest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CORBATEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CORBATEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 corbatest \- Test of EMBL corba retrieval
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBcorbatest\fR\ 'u
 \fBcorbatest\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBcorbatest\fR\ 'u
 \fBcorbatest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cpgplot.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CPGPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CPGPLOT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cpgplot \- Identify and plot CpG islands in nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBcpgplot\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBcpgplot\fR\ 'u
 \fBcpgplot\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -94,11 +102,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cpgreport.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CPGREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CPGREPORT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-cpgreport \- Identify and report CpG-rich regions in nucleotide sequence(s)
+cpgreport \- Identify and report CpG\-rich regions in nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBcpgreport\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBcpgreport\fR\ 'u
 \fBcpgreport\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cusp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cusp.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cusp.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CUSP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CUSP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cusp \- Create a codon usage table from nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBcusp\fR\ 'u
 \fBcusp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 5
+.HP \w'\fBcusp\fR\ 'u
 \fBcusp\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cutgextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CUTGEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CUTGEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cutgextract \- Extract codon usage tables from from CUTG database
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBcutgextract\fR\ 'u
 \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
-.HP 12
+.HP \w'\fBcutgextract\fR\ 'u
 \fBcutgextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/cutseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/cutseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/cutseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "CUTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "CUTSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 cutseq \- Removes a section from a sequence
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBcutseq\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBcutseq\fR\ 'u
 \fBcutseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dan.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dan.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dan \- Calculates nucleic acid melting temperature
 .SH "SYNOPSIS"
-.HP 4
+.HP \w'\fBdan\fR\ 'u
 \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
-.HP 4
+.HP \w'\fBdan\fR\ 'u
 \fBdan\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -118,11 +126,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbiblast.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBIBLAST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBIBLAST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbiblast \- Index a BLAST database
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdbiblast\fR\ 'u
 \fBdbiblast\fR \fB\-dbname\ \fR\fB\fIstring\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\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blastversion\ \fR\fB\fIlist\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-sourcefile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
-.HP 9
+.HP \w'\fBdbiblast\fR\ 'u
 \fBdbiblast\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -112,11 +120,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbifasta.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBIFASTA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBIFASTA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbifasta \- Index a fasta file database
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdbifasta\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBdbifasta\fR\ 'u
 \fBdbifasta\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -103,11 +111,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbiflat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBIFLAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBIFLAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbiflat \- Index a flat file database
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdbiflat\fR\ 'u
 \fBdbiflat\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
-.HP 8
+.HP \w'\fBdbiflat\fR\ 'u
 \fBdbiflat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -103,11 +111,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbigcg.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBIGCG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBIGCG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbigcg \- Index a GCG formatted database
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBdbigcg\fR\ 'u
 \fBdbigcg\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
-.HP 7
+.HP \w'\fBdbigcg\fR\ 'u
 \fBdbigcg\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -103,11 +111,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxfasta.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBXFASTA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBXFASTA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbxfasta \- Index a fasta file database using b+tree indices
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdbxfasta\fR\ 'u
 \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
+.HP \w'\fBdbxfasta\fR\ 'u
 \fBdbxfasta\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -88,11 +96,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxflat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBXFLAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBXFLAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbxflat \- Index a flat file database using b+tree indices
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdbxflat\fR\ 'u
 \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
+.HP \w'\fBdbxflat\fR\ 'u
 \fBdbxflat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -88,11 +96,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxgcg.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBXGCG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBXGCG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbxgcg \- Index a GCG formatted database using b+tree indices
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBdbxgcg\fR\ 'u
 \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
+.HP \w'\fBdbxgcg\fR\ 'u
 \fBdbxgcg\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -88,11 +96,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Added: trunk/packages/emboss/trunk/debian/manpages/dbxreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxreport.1e	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxreport.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -0,0 +1,78 @@
+'\" t
+.\"     Title: DBXREPORT
+.\"    Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
+.\"
+.TH "DBXREPORT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxreport \- Validate index and report internals for dbx databases
+.SH "SYNOPSIS"
+.HP \w'\fBdbxreport\fR\ 'u
+\fBdbxreport\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-idtype\ \fR\fB\fIlist\fR\fR \fB\-fullreport\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxreport\fR\ 'u
+\fBdbxreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-indexdir\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-idtype\fR \fIlist\fR
+.RS 4
+Default value: all
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.PP
+\fB\-fullreport\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.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
+dbxreport 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\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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/dbxstat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dbxstat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DBXSTAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DBXSTAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dbxstat \- Dump statistics for dbx databases
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdbxstat\fR\ 'u
 \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
+.HP \w'\fBdbxstat\fR\ 'u
 \fBdbxstat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -64,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/degapseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/degapseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/degapseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEGAPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEGAPSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-degapseq \- Removes non-alphabetic (e.g. gap) characters from sequences
+degapseq \- Removes non\-alphabetic (e\&.g\&. gap) characters from sequences
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdegapseq\fR\ 'u
 \fBdegapseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 9
+.HP \w'\fBdegapseq\fR\ 'u
 \fBdegapseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demoalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demoalign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demoalign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demoalign \- Reads a sequence set, writes an alignment file
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBdemoalign\fR\ 'u
 \fBdemoalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-floatmatrix\ \fR\fB\fImatrixf\fR\fR] [\fB\-intmatrix\ \fR\fB\fImatrix\fR\fR] \fB\-dofloat\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
-.HP 10
+.HP \w'\fBdemoalign\fR\ 'u
 \fBdemoalign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demofeatures.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOFEATURES" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOFEATURES" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demofeatures \- Demonstration of the feature functions
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBdemofeatures\fR\ 'u
 \fBdemofeatures\fR \fB\-typesort\ \fR\fB\fIboolean\fR\fR \fB\-startsort\ \fR\fB\fIboolean\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
-.HP 13
+.HP \w'\fBdemofeatures\fR\ 'u
 \fBdemofeatures\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -50,11 +58,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demolist.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demolist.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demolist.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOLIST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOLIST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demolist \- Demonstration of the list functions
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBdemolist\fR\ 'u
 \fBdemolist\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
-.HP 9
+.HP \w'\fBdemolist\fR\ 'u
 \fBdemolist\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -39,11 +47,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demoreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demoreport.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demoreport.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOREPORT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demoreport \- Reads a sequence and feature table, writes a report
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBdemoreport\fR\ 'u
 \fBdemoreport\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 11
+.HP \w'\fBdemoreport\fR\ 'u
 \fBdemoreport\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demosequence.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demosequence.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demosequence.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOSEQUENCE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSEQUENCE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demosequence \- Demonstration of the sequence functions
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBdemosequence\fR\ 'u
 \fBdemosequence\fR
-.HP 13
+.HP \w'\fBdemosequence\fR\ 'u
 \fBdemosequence\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -34,11 +42,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demostring.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demostring.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demostring.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOSTRING" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSTRING" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demostring \- Demonstration of the string functions
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBdemostring\fR\ 'u
 \fBdemostring\fR \fB\-instring\ \fR\fB\fIstring\fR\fR
-.HP 11
+.HP \w'\fBdemostring\fR\ 'u
 \fBdemostring\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demostringnew.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOSTRINGNEW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOSTRINGNEW" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-demostringnew \- Illustrates use of the AJAX string library.
+demostringnew \- Illustrates use of the AJAX string library\&.
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBdemostringnew\fR\ 'u
 \fBdemostringnew\fR
-.HP 14
+.HP \w'\fBdemostringnew\fR\ 'u
 \fBdemostringnew\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -34,11 +42,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/demotable.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/demotable.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/demotable.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DEMOTABLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DEMOTABLE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 demotable \- Demonstration of the table functions
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBdemotable\fR\ 'u
 \fBdemotable\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
-.HP 10
+.HP \w'\fBdemotable\fR\ 'u
 \fBdemotable\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -39,11 +47,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/density.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/density.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/density.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DENSITY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DENSITY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .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
+.HP \w'\fBdensity\fR\ 'u
+\fBdensity\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-display\ \fR\fB\fIlist\fR\fR] \fB\-isdual\ \fR\fB\fIvariable\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBdensity\fR\ 'u
 \fBdensity\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -33,26 +41,21 @@
 .RS 4
 Default value: 100
 .RE
-.SS "Output section"
 .PP
-\fB\-quad\fR \fItoggle\fR
+\fB\-display\fR \fIlist\fR
 .RS 4
-Default value: N
+Default value: none
 .RE
+.SS "Output section"
 .PP
-\fB\-dual\fR \fItoggle\fR
+\fB\-isdual\fR \fIvariable\fR
 .RS 4
-Default value: N
 .RE
 .PP
-\fB\-qgraph\fR \fIxygraph\fR
+\fB\-graph\fR \fIxygraph\fR
 .RS 4
 .RE
 .PP
-\fB\-dgraph\fR \fIxygraph\fR
-.RS 4
-.RE
-.PP
 \fB\-outfile\fR \fIreport\fR
 .RS 4
 .RE
@@ -67,11 +70,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/descseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/descseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/descseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DESCSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DESCSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-descseq \- Alter the name or description of a sequence.
+descseq \- Alter the name or description of a sequence\&.
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdescseq\fR\ 'u
 \fBdescseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-description\ \fR\fB\fIstring\fR\fR] \fB\-append\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 8
+.HP \w'\fBdescseq\fR\ 'u
 \fBdescseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/diffseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/diffseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/diffseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DIFFSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DIFFSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 diffseq \- Compare and report features of two similar sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdiffseq\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBdiffseq\fR\ 'u
 \fBdiffseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/digest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/digest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/digest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DIGEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DIGEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 digest \- Reports on protein proteolytic enzyme or reagent cleavage sites
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBdigest\fR\ 'u
 \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
+.HP \w'\fBdigest\fR\ 'u
 \fBdigest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -85,11 +93,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/distmat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/distmat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/distmat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DISTMAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DISTMAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 distmat \- Create a distance matrix from a multiple sequence alignment
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdistmat\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBdistmat\fR\ 'u
 \fBdistmat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -81,11 +89,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dotmatcher.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DOTMATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DOTMATCHER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dotmatcher \- Draw a threshold dotplot of two sequences
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBdotmatcher\fR\ 'u
 \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
-.HP 11
+.HP \w'\fBdotmatcher\fR\ 'u
 \fBdotmatcher\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -72,11 +80,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dotpath.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dotpath.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dotpath.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DOTPATH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DOTPATH" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-dotpath \- Draw a non-overlapping wordmatch dotplot of two sequences
+dotpath \- Draw a non\-overlapping wordmatch dotplot of two sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBdotpath\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBdotpath\fR\ 'u
 \fBdotpath\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dottup.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dottup.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dottup.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DOTTUP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DOTTUP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dottup \- Displays a wordmatch dotplot of two sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBdottup\fR\ 'u
 \fBdottup\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \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 \fB\-boxit\ \fR\fB\fIboolean\fR\fR
-.HP 7
+.HP \w'\fBdottup\fR\ 'u
 \fBdottup\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -67,11 +75,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/dreg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/dreg.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/dreg.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "DREG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "DREG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 dreg \- Regular expression search of nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBdreg\fR\ 'u
 \fBdreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 5
+.HP \w'\fBdreg\fR\ 'u
 \fBdreg\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/edialign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/edialign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/edialign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EDIALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EDIALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 edialign \- Local multiple alignment of sequences
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBedialign\fR\ 'u
 \fBedialign\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-nucmode\ \fR\fB\fIlist\fR\fR \fB\-revcomp\ \fR\fB\fIboolean\fR\fR [\fB\-overlapw\ \fR\fB\fIselection\fR\fR] [\fB\-linkage\ \fR\fB\fIlist\fR\fR] [\fB\-maxfragl\ \fR\fB\fIinteger\fR\fR] \fB\-fragmat\ \fR\fB\fIboolean\fR\fR \fB\-fragsim\ \fR\fB\fIinteger\fR\fR [\fB\-itscore\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mask\ \fR\fB\fIboolean\fR\fR \fB\-dostars\ \fR\fB\fIboolean\fR\fR \fB\-starnum\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 9
+.HP \w'\fBedialign\fR\ 'u
 \fBedialign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -108,11 +116,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/einverted.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/einverted.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/einverted.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EINVERTED" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EINVERTED" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 einverted \- Finds inverted repeats in nucleotide sequences
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBeinverted\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBeinverted\fR\ 'u
 \fBeinverted\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -75,11 +83,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/embossdata.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/embossdata.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/embossdata.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EMBOSSDATA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EMBOSSDATA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 embossdata \- Find and retrieve EMBOSS data files
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBembossdata\fR\ 'u
 \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]
-.HP 11
+.HP \w'\fBembossdata\fR\ 'u
 \fBembossdata\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/embossversion.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/embossversion.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/embossversion.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EMBOSSVERSION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EMBOSSVERSION" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-embossversion \- Writes the current EMBOSS version number to a file
+embossversion \- Reports the current EMBOSS version number
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBembossversion\fR\ 'u
 \fBembossversion\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
-.HP 14
+.HP \w'\fBembossversion\fR\ 'u
 \fBembossversion\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/emma.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/emma.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/emma.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EMMA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EMMA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 emma \- Multiple sequence alignment (ClustalW wrapper)
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBemma\fR\ 'u
 \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
-.HP 5
+.HP \w'\fBemma\fR\ 'u
 \fBemma\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -187,11 +195,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/emowse.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/emowse.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/emowse.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EMOWSE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EMOWSE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 emowse \- Search protein sequences by digest fragment molecular weight
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBemowse\fR\ 'u
 \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
+.HP \w'\fBemowse\fR\ 'u
 \fBemowse\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -88,11 +96,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/entrails.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/entrails.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/entrails.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ENTRAILS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ENTRAILS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 entrails \- Reports the internal data from the EMBOSS code
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBentrails\fR\ 'u
 \fBentrails\fR [\fB\-fullreport\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBentrails\fR\ 'u
 \fBentrails\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/entret.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/entret.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/entret.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ENTRET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ENTRET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 entret \- Retrieves sequence entries from flatfile databases and files
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBentret\fR\ 'u
 \fBentret\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBentret\fR\ 'u
 \fBentret\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/epestfind.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/epestfind.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/epestfind.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EPESTFIND" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EPESTFIND" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 epestfind \- Finds PEST motifs as potential proteolytic cleavage sites
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBepestfind\fR\ 'u
 \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
+.HP \w'\fBepestfind\fR\ 'u
 \fBepestfind\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -97,11 +105,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/eprimer3.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EPRIMER3" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EPRIMER3" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 eprimer3 \- Picks PCR primers and hybridization oligos
 .SH "SYNOPSIS"
-.HP 9
-\fBeprimer3\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-oligomishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-target\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-productosize\ \fR\fB\fIinteger\fR\fR \fB\-productsizerange\ \fR\fB\fIrange\fR\fR \fB\-productotm\ \fR\fB\fIfloat\fR\fR \fB\-productmintm\ \fR\fB\fIfloat\fR\fR \fB\-productmaxtm\ \fR\fB\fIfloat\fR\fR \fB\-oligoexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-oligoosize\ \fR\fB\fIinteger\fR\fR \fB\-oligominsize\ \fR\fB\fIinteger\fR\fR \fB\-oligomaxsize\ \fR\fB\fIinteger\fR\fR \fB\-oligootm\ \fR\fB\fIfloat\fR\fR \fB\-oligomintm\ \fR\fB\fIfloat\fR\fR \fB\-oligomaxtm\ \fR\fB\fIfloat\fR\fR \fB\-oligoogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-oligomingc\ \fR\fB\fIfloat\fR\fR \fB\-oligomaxgc\ \fR\fB\fIfloat\fR\fR \fB\-oligosaltconc\ \fR\fB\fIfloat\fR\fR \fB\-oligodnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oligoselfany\ \fR\fB\fIfloat\fR\fR \fB\-oligoselfend\ \fR\fB\fIfloat\fR\fR \fB\-oligomaxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-oligomaxmishyb\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBeprimer3\fR\ 'u
+\fBeprimer3\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-mishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-target\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-psizeopt\ \fR\fB\fIinteger\fR\fR \fB\-prange\ \fR\fB\fIrange\fR\fR \fB\-ptmopt\ \fR\fB\fIfloat\fR\fR \fB\-ptmmin\ \fR\fB\fIfloat\fR\fR \fB\-ptmmax\ \fR\fB\fIfloat\fR\fR \fB\-oexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-osizeopt\ \fR\fB\fIinteger\fR\fR \fB\-ominsize\ \fR\fB\fIinteger\fR\fR \fB\-omaxsize\ \fR\fB\fIinteger\fR\fR \fB\-otmopt\ \fR\fB\fIfloat\fR\fR \fB\-otmmin\ \fR\fB\fIfloat\fR\fR \fB\-otmmax\ \fR\fB\fIfloat\fR\fR \fB\-ogcopt\ \fR\fB\fIfloat\fR\fR \fB\-ogcmin\ \fR\fB\fIfloat\fR\fR \fB\-ogcmax\ \fR\fB\fIfloat\fR\fR \fB\-osaltconc\ \fR\fB\fIfloat\fR\fR \fB\-odnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oanyself\ \fR\fB\fIfloat\fR\fR \fB\-oendself\ \fR\fB\fIfloat\fR\fR \fB\-opolyxmax\ \fR\fB\fIinteger\fR\fR \fB\-omishybmax\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBeprimer3\fR\ 'u
 \fBeprimer3\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,7 +52,7 @@
 An \'internal oligo\' is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification\&. Default value: N
 .RE
 .PP
-\fB\-oligomishyblibraryfile\fR \fIinfile\fR
+\fB\-mishyblibraryfile\fR \fIinfile\fR
 .RS 4
 Similar to MISPRIMING\-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them\&. The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then EPrimer3 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL\-OLIGO\-MAX\-MISHYB\&. (The maximum value of the weight is arbitrarily set to 12\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \'id line\' that starts with \'>\'\&. The contents of the id line is \'slightly restricted\' in that EPrimer3 parses everything after any optional asterisk (\'*\') as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \'>\' or the end of the file\&. Whitespace and newlines are ignored\&. Characters \'A\', \'T\', \'G\', \'C\', \'a\', \'t\', \'g\', \'c\' are retained and any other character is converted to \'N\' (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \'N\')\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no library should be used\&.
 .RE
@@ -159,33 +167,33 @@
 .RE
 .SS "Product options"
 .PP
-\fB\-productosize\fR \fIinteger\fR
+\fB\-psizeopt\fR \fIinteger\fR
 .RS 4
 The optimum size for the PCR product\&. 0 indicates that there is no optimum product size\&. Default value: 200
 .RE
 .PP
-\fB\-productsizerange\fR \fIrange\fR
+\fB\-prange\fR \fIrange\fR
 .RS 4
 The associated values specify the lengths of the product that the user wants the primers to create, and is a space separated list of elements of the form (x)\-(y) where an (x)\-(y) pair is a legal range of lengths for the product\&. For example, if one wants PCR products to be between 100 to 150 bases (inclusive) then one would set this parameter to 100\-150\&. If one desires PCR products in either the range from 100 to 150 bases or in the range from 200 to 250 bases then one would set this parameter to 100\-150 200\-250\&. EPrimer3 favors ranges to the left side of the parameter string\&. EPrimer3 will return legal primers pairs in the first range regardless the value of the objective function for these pairs\&. Only if there are an insufficient number of primers in the first range will EPrimer3 return primers in a subsequent range\&. Default value: 100\-300
 .RE
 .PP
-\fB\-productotm\fR \fIfloat\fR
+\fB\-ptmopt\fR \fIfloat\fR
 .RS 4
 The optimum melting temperature for the PCR product\&. 0 indicates that there is no optimum temperature\&. Default value: 0\&.0
 .RE
 .PP
-\fB\-productmintm\fR \fIfloat\fR
+\fB\-ptmmin\fR \fIfloat\fR
 .RS 4
 The minimum allowed melting temperature of the amplicon\&. Please see the documentation on the maximum melting temperature of the product for details\&. Default value: \-1000000\&.0
 .RE
 .PP
-\fB\-productmaxtm\fR \fIfloat\fR
+\fB\-ptmmax\fR \fIfloat\fR
 .RS 4
 The maximum allowed melting temperature of the amplicon\&. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11\&.46 (1989, CSHL Press)\&. Tm = 81\&.5 + 16\&.6(log10([Na+])) + \&.41*(%GC) \- 600/length Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence\&. A similar formula is used by the prime primer selection program in GCG http://www\&.gcg\&.com), which instead uses 675\&.0/length in the last term (after F\&. Baldino, Jr, M\&.\-F\&. Chesselet, and M\&.E\&. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms)\&. The formulas here and in Baldino et al\&. assume Na+ rather than K+\&. According to J\&.G\&. Wetmur, Critical Reviews in BioChem\&. and Mol\&. Bio\&. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to \&.2 M Na+\&. EPrimer3 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature\&. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions\&. Default value: 1000000\&.0
 .RE
 .SS "Internal oligo input"
 .PP
-\fB\-oligoexcludedregion\fR \fIrange\fR
+\fB\-oexcludedregion\fR \fIrange\fR
 .RS 4
 Middle oligos may not overlap any region specified by this tag\&. The associated value must be a space\-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last\&. Often one would make Target regions excluded regions for internal oligos\&.
 .RE
@@ -196,77 +204,77 @@
 .RE
 .SS "Internal oligo options"
 .PP
-\fB\-oligoosize\fR \fIinteger\fR
+\fB\-osizeopt\fR \fIinteger\fR
 .RS 4
 Optimum length (in bases) of an internal oligo\&. EPrimer3 will attempt to pick primers close to this length\&. Default value: 20
 .RE
 .PP
-\fB\-oligominsize\fR \fIinteger\fR
+\fB\-ominsize\fR \fIinteger\fR
 .RS 4
 Minimum acceptable length of an internal oligo\&. Must be greater than 0 and less than or equal to INTERNAL\-OLIGO\-MAX\-SIZE\&. Default value: 18
 .RE
 .PP
-\fB\-oligomaxsize\fR \fIinteger\fR
+\fB\-omaxsize\fR \fIinteger\fR
 .RS 4
 Maximum acceptable length (in bases) of an internal oligo\&. Currently this parameter cannot be larger than 35\&. This limit is governed by maximum oligo size for which EPrimer3\'s melting\-temperature is valid\&. Default value: 27
 .RE
 .PP
-\fB\-oligootm\fR \fIfloat\fR
+\fB\-otmopt\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 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
+\fB\-otmmin\fR \fIfloat\fR
 .RS 4
 Minimum acceptable melting temperature(Celsius) for an internal oligo\&. Default value: 57\&.0
 .RE
 .PP
-\fB\-oligomaxtm\fR \fIfloat\fR
+\fB\-otmmax\fR \fIfloat\fR
 .RS 4
 Maximum acceptable melting temperature (Celsius) for an internal oligo\&. Default value: 63\&.0
 .RE
 .PP
-\fB\-oligoogcpercent\fR \fIfloat\fR
+\fB\-ogcopt\fR \fIfloat\fR
 .RS 4
 Internal oligo optimum GC percent\&. Default value: 50\&.0
 .RE
 .PP
-\fB\-oligomingc\fR \fIfloat\fR
+\fB\-ogcmin\fR \fIfloat\fR
 .RS 4
 Minimum allowable percentage of Gs and Cs in an internal oligo\&. Default value: 20\&.0
 .RE
 .PP
-\fB\-oligomaxgc\fR \fIfloat\fR
+\fB\-ogcmax\fR \fIfloat\fR
 .RS 4
 Maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer\&. Default value: 80\&.0
 .RE
 .PP
-\fB\-oligosaltconc\fR \fIfloat\fR
+\fB\-osaltconc\fR \fIfloat\fR
 .RS 4
 The millimolar concentration of salt (usually KCl) in the hybridization\&. EPrimer3 uses this argument to calculate internal oligo melting temperatures\&. Default value: 50\&.0
 .RE
 .PP
-\fB\-oligodnaconc\fR \fIfloat\fR
+\fB\-odnaconc\fR \fIfloat\fR
 .RS 4
 The nanomolar concentration of annealing internal oligo in the hybridization\&. Default value: 50\&.0
 .RE
 .PP
-\fB\-oligoselfany\fR \fIfloat\fR
+\fB\-oanyself\fR \fIfloat\fR
 .RS 4
 The maximum allowable local alignment score when testing an internal oligo for (local) self\-complementarity\&. Local self\-complementarity is taken to predict the tendency of oligos to anneal to themselves The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\' ATCGNA 3\' || | | 3\' TA\-CGT 5\' is allowed (and yields a score of 1\&.75), but the alignment 5\' ATCCGNA 3\' || | | 3\' TA\-\-CGT 5\' is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 12\&.00
 .RE
 .PP
-\fB\-oligoselfend\fR \fIfloat\fR
+\fB\-oendself\fR \fIfloat\fR
 .RS 4
 The maximum allowable 3\'\-anchored global alignment score when testing a single oligo for self\-complementarity\&. The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\'\-anchored global alignment between two oligos\&. In order to estimate 3\'\-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5\' to 3\'\&. INTERNAL\-OLIGO\-SELF\-END is meaningless when applied to internal oligos used for hybridization\-based detection, since primer\-dimer will not occur\&. We recommend that INTERNAL\-OLIGO\-SELF\-END be set at least as high as INTERNAL\-OLIGO\-SELF\-ANY\&. Default value: 12\&.00
 .RE
 .PP
-\fB\-oligomaxpolyx\fR \fIinteger\fR
+\fB\-opolyxmax\fR \fIinteger\fR
 .RS 4
 The maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA\&. Default value: 5
 .RE
 .PP
-\fB\-oligomaxmishyb\fR \fIfloat\fR
+\fB\-omishybmax\fR \fIfloat\fR
 .RS 4
 Similar to MAX\-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL\-OLIGO\-MISHYB\-LIBRARY\&. Default value: 12\&.0
 .RE
@@ -338,11 +346,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/equicktandem.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EQUICKTANDEM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EQUICKTANDEM" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 equicktandem \- Finds tandem repeats in nucleotide sequences
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBequicktandem\fR\ 'u
 \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
-.HP 13
+.HP \w'\fBequicktandem\fR\ 'u
 \fBequicktandem\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/est2genome.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/est2genome.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/est2genome.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EST2GENOME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EST2GENOME" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 11
+.HP \w'\fBest2genome\fR\ 'u
+\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\-usesplice\ \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
+.HP \w'\fBest2genome\fR\ 'u
 \fBest2genome\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,7 +77,7 @@
 Reverse the orientation of the EST sequence
 .RE
 .PP
-\fB\-splice\fR \fIboolean\fR
+\fB\-usesplice\fR \fIboolean\fR
 .RS 4
 Use donor and acceptor splice sites\&. If you want to ignore donor\-acceptor sites then set this to be false\&. Default value: Y
 .RE
@@ -123,11 +131,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/etandem.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/etandem.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/etandem.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ETANDEM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ETANDEM" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 etandem \- Finds tandem repeats in a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBetandem\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBetandem\fR\ 'u
 \fBetandem\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -72,11 +80,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/extractalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractalign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/extractalign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EXTRACTALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 extractalign \- Extract regions from a sequence alignment
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBextractalign\fR\ 'u
 \fBextractalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 13
+.HP \w'\fBextractalign\fR\ 'u
 \fBextractalign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/extractfeat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EXTRACTFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTFEAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 extractfeat \- Extract features from sequence(s)
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBextractfeat\fR\ 'u
 \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
-.HP 12
+.HP \w'\fBextractfeat\fR\ 'u
 \fBextractfeat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -46,7 +54,7 @@
 .PP
 \fB\-type\fR \fIstring\fR
 .RS 4
-By default every feature in the feature table is extracted\&. You can set this to be any feature type you wish to extract\&. See http://www3\&.ebi\&.ac\&.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.ch/txt/userman\&.txt for a list of the Swissprot feature types\&. The type may be wildcarded by using \'*\'\&. If you wish to extract more than one type, separate their names with the character \'|\', eg: *UTR | intron Default value: *
+By default every feature in the feature table is extracted\&. You can set this to be any feature type you wish to extract\&. See http://www\&.ebi\&.ac\&.uk/Services/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www\&.uniprot\&.org/manual/sequence_annotation for a list of the Uniprot feature types\&. The type may be wildcarded by using \'*\'\&. If you wish to extract more than one type, separate their names with the character \'|\', eg: *UTR | intron Default value: *
 .RE
 .PP
 \fB\-sense\fR \fIinteger\fR
@@ -56,12 +64,12 @@
 .PP
 \fB\-minscore\fR \fIfloat\fR
 .RS 4
-If this is greater than or equal to the maximum score, then any score is permitted Default value: 0\&.0
+Minimum score of feature to extract (see also maxscore) Default value: 0\&.0
 .RE
 .PP
 \fB\-maxscore\fR \fIfloat\fR
 .RS 4
-If this is less than or equal to the maximum score, then any score is permitted Default value: 0\&.0
+Maximum score of feature to extract\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
 .RE
 .PP
 \fB\-tag\fR \fIstring\fR
@@ -104,11 +112,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/extractseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/extractseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/extractseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "EXTRACTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "EXTRACTSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 extractseq \- Extract regions from a sequence
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBextractseq\fR\ 'u
 \fBextractseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-separate\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 11
+.HP \w'\fBextractseq\fR\ 'u
 \fBextractseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -55,11 +63,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/featcopy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/featcopy.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/featcopy.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FEATCOPY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FEATCOPY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 featcopy \- Reads and writes a feature table
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBfeatcopy\fR\ 'u
 \fBfeatcopy\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
-.HP 9
+.HP \w'\fBfeatcopy\fR\ 'u
 \fBfeatcopy\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/featreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/featreport.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/featreport.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FEATREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FEATREPORT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 featreport \- Reads and writes a feature table
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBfeatreport\fR\ 'u
 \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
+.HP \w'\fBfeatreport\fR\ 'u
 \fBfeatreport\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/findkm.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/findkm.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/findkm.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FINDKM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FINDKM" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 findkm \- Calculate and plot enzyme reaction data
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBfindkm\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBfindkm\fR\ 'u
 \fBfindkm\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -53,11 +61,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/freak.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/freak.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/freak.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FREAK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FREAK" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 freak \- Generate residue/base frequency table or plot
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBfreak\fR\ 'u
 \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
-.HP 6
+.HP \w'\fBfreak\fR\ 'u
 \fBfreak\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzznuc.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FUZZNUC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZNUC" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 fuzznuc \- Search for patterns in nucleotide sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBfuzznuc\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBfuzznuc\fR\ 'u
 \fBfuzznuc\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzzpro.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FUZZPRO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZPRO" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 fuzzpro \- Search for patterns in protein sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBfuzzpro\fR\ 'u
 \fBfuzzpro\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 8
+.HP \w'\fBfuzzpro\fR\ 'u
 \fBfuzzpro\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/fuzztran.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "FUZZTRAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "FUZZTRAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 fuzztran \- Search for patterns in protein sequences (translated)
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBfuzztran\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBfuzztran\fR\ 'u
 \fBfuzztran\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/garnier.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/garnier.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/garnier.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "GARNIER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "GARNIER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 garnier \- Predicts protein secondary structure using GOR method
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBgarnier\fR\ 'u
 \fBgarnier\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-idc\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 8
+.HP \w'\fBgarnier\fR\ 'u
 \fBgarnier\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/geecee.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/geecee.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/geecee.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "GEECEE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "GEECEE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 geecee \- Calculate fractional GC content of nucleic acid sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBgeecee\fR\ 'u
 \fBgeecee\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBgeecee\fR\ 'u
 \fBgeecee\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/getorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/getorf.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/getorf.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "GETORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "GETORF" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 getorf \- Finds and extracts open reading frames (ORFs)
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBgetorf\fR\ 'u
 \fBgetorf\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-find\ \fR\fB\fIlist\fR\fR] \fB\-methionine\ \fR\fB\fIboolean\fR\fR \fB\-circular\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-flanking\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 7
+.HP \w'\fBgetorf\fR\ 'u
 \fBgetorf\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -84,11 +92,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/giep.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/giep.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/giep.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "GIEP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "GIEP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 giep \- Calculates the isoelectric point of a protein
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBgiep\fR\ 'u
 \fBgiep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-step\ \fR\fB\fIfloat\fR\fR \fB\-amino\ \fR\fB\fIinteger\fR\fR \fB\-termini\ \fR\fB\fIboolean\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
-.HP 5
+.HP \w'\fBgiep\fR\ 'u
 \fBgiep\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -73,11 +81,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/helixturnhelix.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "HELIXTURNHELIX" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "HELIXTURNHELIX" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-helixturnhelix \- Identify nucleic acid-binding motifs in protein sequences
+helixturnhelix \- Identify nucleic acid\-binding motifs in protein sequences
 .SH "SYNOPSIS"
-.HP 15
+.HP \w'\fBhelixturnhelix\fR\ 'u
 \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
-.HP 15
+.HP \w'\fBhelixturnhelix\fR\ 'u
 \fBhelixturnhelix\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/histogramtest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "HISTOGRAMTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "HISTOGRAMTEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 histogramtest \- Test of graphics
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBhistogramtest\fR\ 'u
 \fBhistogramtest\fR \fB\-sets\ \fR\fB\fIinteger\fR\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-bins\ \fR\fB\fIinteger\fR\fR \fB\-xstart\ \fR\fB\fIinteger\fR\fR \fB\-xend\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
-.HP 14
+.HP \w'\fBhistogramtest\fR\ 'u
 \fBhistogramtest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/hmoment.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/hmoment.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/hmoment.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "HMOMENT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "HMOMENT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 hmoment \- Calculate and plot hydrophobic moment for protein sequence(s)
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBhmoment\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBhmoment\fR\ 'u
 \fBhmoment\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -79,11 +87,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/iep.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/iep.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/iep.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "IEP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "IEP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 4
+.HP \w'\fBiep\fR\ 'u
+\fBiep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-amino\ \fR\fB\fIinteger\fR\fR] [\fB\-carboxyl\ \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
+.HP \w'\fBiep\fR\ 'u
 \fBiep\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -34,6 +42,11 @@
 Default value: 1
 .RE
 .PP
+\fB\-carboxyl\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
 \fB\-termini\fR \fIboolean\fR
 .RS 4
 Default value: Y
@@ -82,11 +95,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/infoalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infoalign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/infoalign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "INFOALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "INFOALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 infoalign \- Display basic information about a multiple sequence alignment
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBinfoalign\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBinfoalign\fR\ 'u
 \fBinfoalign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -141,11 +149,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/infobase.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infobase.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/infobase.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "INFOBASE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "INFOBASE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 infobase \- Return information on a given nucleotide base
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBinfobase\fR\ 'u
 \fBinfobase\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBinfobase\fR\ 'u
 \fBinfobase\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/inforesidue.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "INFORESIDUE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "INFORESIDUE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 inforesidue \- Return information on a given amino acid residue
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBinforesidue\fR\ 'u
 \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
+.HP \w'\fBinforesidue\fR\ 'u
 \fBinforesidue\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -57,11 +65,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/infoseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/infoseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/infoseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "INFOSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "INFOSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 infoseq \- Display basic information about sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBinfoseq\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBinfoseq\fR\ 'u
 \fBinfoseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -120,11 +128,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/intconv.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/intconv.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/intconv.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "INTCONV" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "INTCONV" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 intconv \- Convert ints to ajints and longs to ajlongs
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBintconv\fR\ 'u
 \fBintconv\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 8
+.HP \w'\fBintconv\fR\ 'u
 \fBintconv\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/isochore.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/isochore.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/isochore.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ISOCHORE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ISOCHORE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 isochore \- Plots isochores in DNA sequences
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBisochore\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBisochore\fR\ 'u
 \fBisochore\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/jaspextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "JASPEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "JASPEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 jaspextract \- Extract data from JASPAR
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBjaspextract\fR\ 'u
 \fBjaspextract\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR
-.HP 12
+.HP \w'\fBjaspextract\fR\ 'u
 \fBjaspextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -39,11 +47,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/jaspscan.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "JASPSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "JASPSCAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 jaspscan \- Scans DNA sequences for transcription factors
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBjaspscan\fR\ 'u
 \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
+.HP \w'\fBjaspscan\fR\ 'u
 \fBjaspscan\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -70,11 +78,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/lindna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/lindna.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/lindna.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "LINDNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "LINDNA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 lindna \- Draws linear maps of DNA constructs
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBlindna\fR\ 'u
 \fBlindna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-intersymbol\ \fR\fB\fIselection\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-margin\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR
-.HP 7
+.HP \w'\fBlindna\fR\ 'u
 \fBlindna\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -130,11 +138,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/listor.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/listor.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/listor.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "LISTOR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "LISTOR" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 listor \- Write a list file of the logical OR of two sets of sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBlistor\fR\ 'u
 \fBlistor\fR \fB\-firstsequences\ \fR\fB\fIseqset\fR\fR \fB\-secondsequences\ \fR\fB\fIseqset\fR\fR [\fB\-operator\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBlistor\fR\ 'u
 \fBlistor\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/makenucseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MAKENUCSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MAKENUCSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 makenucseq \- Create random nucleotide sequences
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBmakenucseq\fR\ 'u
 \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
-.HP 11
+.HP \w'\fBmakenucseq\fR\ 'u
 \fBmakenucseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -70,11 +78,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/makeprotseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MAKEPROTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MAKEPROTSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 makeprotseq \- Create random protein sequences
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBmakeprotseq\fR\ 'u
 \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
-.HP 12
+.HP \w'\fBmakeprotseq\fR\ 'u
 \fBmakeprotseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -70,11 +78,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/marscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/marscan.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/marscan.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MARSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MARSCAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 marscan \- Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBmarscan\fR\ 'u
 \fBmarscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 8
+.HP \w'\fBmarscan\fR\ 'u
 \fBmarscan\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/maskambignuc.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MASKAMBIGNUC" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MASKAMBIGNUC" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 maskambignuc \- Masks all ambiguity characters in nucleotide sequences with N
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBmaskambignuc\fR\ 'u
 \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
+.HP \w'\fBmaskambignuc\fR\ 'u
 \fBmaskambignuc\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/maskambigprot.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MASKAMBIGPROT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MASKAMBIGPROT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 maskambigprot \- Masks all ambiguity characters in protein sequences with X
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBmaskambigprot\fR\ 'u
 \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
+.HP \w'\fBmaskambigprot\fR\ 'u
 \fBmaskambigprot\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/maskfeat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MASKFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MASKFEAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 maskfeat \- Write a sequence with masked features
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBmaskfeat\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBmaskfeat\fR\ 'u
 \fBmaskfeat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/maskseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/maskseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/maskseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MASKSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MASKSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 maskseq \- Write a sequence with masked regions
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBmaskseq\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBmaskseq\fR\ 'u
 \fBmaskseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/matcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/matcher.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/matcher.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MATCHER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-matcher \- Waterman-Eggert local alignment of two sequences
+matcher \- Waterman\-Eggert local alignment of two sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBmatcher\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBmatcher\fR\ 'u
 \fBmatcher\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -68,11 +76,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/megamerger.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/megamerger.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/megamerger.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MEGAMERGER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MEGAMERGER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 megamerger \- Merge two large overlapping DNA sequences
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBmegamerger\fR\ 'u
 \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
-.HP 11
+.HP \w'\fBmegamerger\fR\ 'u
 \fBmegamerger\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/merger.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/merger.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/merger.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MERGER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MERGER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 merger \- Merge two overlapping sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBmerger\fR\ 'u
 \fBmerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 7
+.HP \w'\fBmerger\fR\ 'u
 \fBmerger\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -67,11 +75,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/msbar.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/msbar.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/msbar.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MSBAR" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MSBAR" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 msbar \- Mutate a sequence
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBmsbar\fR\ 'u
 \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
-.HP 6
+.HP \w'\fBmsbar\fR\ 'u
 \fBmsbar\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -84,11 +92,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/mwcontam.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MWCONTAM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MWCONTAM" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 mwcontam \- Find weights common to multiple molecular weights files
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBmwcontam\fR\ 'u
 \fBmwcontam\fR \fB\-files\ \fR\fB\fIfilelist\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBmwcontam\fR\ 'u
 \fBmwcontam\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/mwfilter.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "MWFILTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "MWFILTER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 mwfilter \- Filter noisy data from molecular weights file
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBmwfilter\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBmwfilter\fR\ 'u
 \fBmwfilter\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/needle.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/needle.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/needle.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NEEDLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NEEDLE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-needle \- Needleman-Wunsch global alignment of two sequences
+needle \- Needleman\-Wunsch global alignment of two sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBneedle\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBneedle\fR\ 'u
 \fBneedle\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -68,11 +76,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/newcoils.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcoils.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/newcoils.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NEWCOILS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCOILS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 newcoils \- Predicts coils protein secondary structure
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBnewcoils\fR\ 'u
 \fBnewcoils\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-weighted\ \fR\fB\fIinteger\fR\fR \fB\-verb\ \fR\fB\fIinteger\fR\fR \fB\-mode\ \fR\fB\fIinteger\fR\fR \fB\-minseg\ \fR\fB\fIinteger\fR\fR \fB\-minp\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBnewcoils\fR\ 'u
 \fBnewcoils\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -76,11 +84,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/newcpgreport.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NEWCPGREPORT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCPGREPORT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 newcpgreport \- Identify CpG islands in nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBnewcpgreport\fR\ 'u
 \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
-.HP 13
+.HP \w'\fBnewcpgreport\fR\ 'u
 \fBnewcpgreport\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/newcpgseek.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NEWCPGSEEK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NEWCPGSEEK" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-newcpgseek \- Identify and report CpG-rich regions in nucleotide sequence(s)
+newcpgseek \- Identify and report CpG\-rich regions in nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBnewcpgseek\fR\ 'u
 \fBnewcpgseek\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
+.HP \w'\fBnewcpgseek\fR\ 'u
 \fBnewcpgseek\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/newseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/newseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/newseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NEWSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NEWSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-newseq \- Create a sequence file from a typed-in sequence
+newseq \- Create a sequence file from a typed\-in sequence
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBnewseq\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBnewseq\fR\ 'u
 \fBnewseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/nohtml.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nohtml.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/nohtml.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NOHTML" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NOHTML" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-nohtml \- Remove mark-up (e.g. HTML tags) from an ASCII text file
+nohtml \- Remove mark\-up (e\&.g\&. HTML tags) from an ASCII text file
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBnohtml\fR\ 'u
 \fBnohtml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBnohtml\fR\ 'u
 \fBnohtml\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -46,11 +54,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/noreturn.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/noreturn.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/noreturn.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NORETURN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NORETURN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 noreturn \- Remove carriage return from ASCII files
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBnoreturn\fR\ 'u
 \fBnoreturn\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-system\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 9
+.HP \w'\fBnoreturn\fR\ 'u
 \fBnoreturn\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/nospace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nospace.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/nospace.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NOSPACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NOSPACE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 nospace \- Remove all whitespace from an ASCII text file
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBnospace\fR\ 'u
 \fBnospace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 8
+.HP \w'\fBnospace\fR\ 'u
 \fBnospace\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -46,11 +54,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/notab.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/notab.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/notab.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NOTAB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NOTAB" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 notab \- Replace tabs with spaces in an ASCII text file
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBnotab\fR\ 'u
 \fBnotab\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 6
+.HP \w'\fBnotab\fR\ 'u
 \fBnotab\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -46,11 +54,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/notseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/notseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/notseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NOTSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NOTSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 notseq \- Write to file a subset of an input stream of sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBnotseq\fR\ 'u
 \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]
-.HP 7
+.HP \w'\fBnotseq\fR\ 'u
 \fBnotseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/nthseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nthseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/nthseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "NTHSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "NTHSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 nthseq \- Write to file a single sequence from an input stream of sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBnthseq\fR\ 'u
 \fBnthseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 7
+.HP \w'\fBnthseq\fR\ 'u
 \fBnthseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Added: trunk/packages/emboss/trunk/debian/manpages/nthseqset.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/nthseqset.1e	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/nthseqset.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: NTHSEQSET
+.\"    Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
+.\"
+.TH "NTHSEQSET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+nthseqset \- Reads and writes (returns) one set of sequences from many
+.SH "SYNOPSIS"
+.HP \w'\fBnthseqset\fR\ 'u
+\fBnthseqset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBnthseqset\fR\ 'u
+\fBnthseqset\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnthseqset\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 \fIseqsetall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-number\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.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
+nthseqset 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\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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/octanol.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/octanol.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/octanol.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "OCTANOL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "OCTANOL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-octanol \- Draw a White-Wimley protein hydropathy plot
+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]
-.HP 8
+.HP \w'\fBoctanol\fR\ 'u
+\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\-plotoctanol\ \fR\fB\fIboolean\fR\fR] [\fB\-plotinterface\ \fR\fB\fIboolean\fR\fR] [\fB\-plotdifference\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBoctanol\fR\ 'u
 \fBoctanol\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,17 +52,17 @@
 .RS 4
 .RE
 .PP
-\fB\-octanolplot\fR \fIboolean\fR
+\fB\-plotoctanol\fR \fIboolean\fR
 .RS 4
 Default value: N
 .RE
 .PP
-\fB\-interfaceplot\fR \fIboolean\fR
+\fB\-plotinterface\fR \fIboolean\fR
 .RS 4
 Default value: N
 .RE
 .PP
-\fB\-differenceplot\fR \fIboolean\fR
+\fB\-plotdifference\fR \fIboolean\fR
 .RS 4
 Default value: Y
 .RE
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/oddcomp.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ODDCOMP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ODDCOMP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 oddcomp \- Identify proteins with specified sequence word composition
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBoddcomp\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBoddcomp\fR\ 'u
 \fBoddcomp\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -66,11 +74,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/origsplitter.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ORIGSPLITTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ORIGSPLITTER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 origsplitter \- Split a sequence into (overlapping) smaller sequences
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBorigsplitter\fR\ 'u
 \fBorigsplitter\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 13
+.HP \w'\fBorigsplitter\fR\ 'u
 \fBorigsplitter\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/origunion.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/origunion.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/origunion.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "ORIGUNION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "ORIGUNION" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 origunion \- Reads sequence fragments and builds one sequence
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBorigunion\fR\ 'u
 \fBorigunion\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 10
+.HP \w'\fBorigunion\fR\ 'u
 \fBorigunion\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/palindrome.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/palindrome.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/palindrome.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PALINDROME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PALINDROME" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 palindrome \- Finds inverted repeats in nucleotide sequence(s)
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBpalindrome\fR\ 'u
 \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
-.HP 11
+.HP \w'\fBpalindrome\fR\ 'u
 \fBpalindrome\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -68,11 +76,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pasteseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PASTESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PASTESEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pasteseq \- Insert one sequence into another
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBpasteseq\fR\ 'u
 \fBpasteseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-pos\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 9
+.HP \w'\fBpasteseq\fR\ 'u
 \fBpasteseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -53,11 +61,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/patmatdb.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PATMATDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATDB" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 patmatdb \- Searches protein sequences with a sequence motif
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBpatmatdb\fR\ 'u
 \fBpatmatdb\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-motif\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 9
+.HP \w'\fBpatmatdb\fR\ 'u
 \fBpatmatdb\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/patmatmotifs.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PATMATMOTIFS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATMOTIFS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 patmatmotifs \- Scan a protein sequence with motifs from the PROSITE database
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBpatmatmotifs\fR\ 'u
 \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
-.HP 13
+.HP \w'\fBpatmatmotifs\fR\ 'u
 \fBpatmatmotifs\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/patmattest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/patmattest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/patmattest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PATMATTEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PATMATTEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 patmattest \- Test of pattern matching
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBpatmattest\fR\ 'u
 \fBpatmattest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-expression\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 11
+.HP \w'\fBpatmattest\fR\ 'u
 \fBpatmattest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepcoil.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPCOIL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPCOIL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pepcoil \- Predicts coiled coil regions in protein sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBpepcoil\fR\ 'u
 \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
+.HP \w'\fBpepcoil\fR\ 'u
 \fBpepcoil\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -64,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepinfo.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPINFO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPINFO" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-pepinfo \- Plot amino acid properties of a protein sequence in parallel.
+pepinfo \- Plot amino acid properties of a protein sequence in parallel\&.
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBpepinfo\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBpepinfo\fR\ 'u
 \fBpepinfo\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -73,11 +81,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepnet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepnet.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepnet.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPNET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPNET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pepnet \- Draw a helical net for a protein sequence
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBpepnet\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBpepnet\fR\ 'u
 \fBpepnet\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepstats.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepstats.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepstats.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPSTATS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPSTATS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pepstats \- Calculates statistics of protein properties
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBpepstats\fR\ 'u
 \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
+.HP \w'\fBpepstats\fR\ 'u
 \fBpepstats\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -64,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwheel.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPWHEEL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWHEEL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pepwheel \- Draw a helical wheel diagram for a protein sequence
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBpepwheel\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBpepwheel\fR\ 'u
 \fBpepwheel\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -79,11 +87,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwindow.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPWINDOW" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWINDOW" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-pepwindow \- Draw a Kyte-Doolittle hydropathy plot for a protein sequence
+pepwindow \- Draw a 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
-.HP 10
+.HP \w'\fBpepwindow\fR\ 'u
+\fBpepwindow\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBpepwindow\fR\ 'u
 \fBpepwindow\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -36,8 +44,13 @@
 .PP
 \fB\-length\fR \fIinteger\fR
 .RS 4
-Default value: 7
+Default value: 19
 .RE
+.PP
+\fB\-normalize\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
 .SS "Output section"
 .PP
 \fB\-graph\fR \fIxygraph\fR
@@ -54,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pepwindowall.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PEPWINDOWALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PEPWINDOWALL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-pepwindowall \- Draw Kyte-Doolittle hydropathy plot for a protein alignment
+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
-.HP 13
+.HP \w'\fBpepwindowall\fR\ 'u
+\fBpepwindowall\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBpepwindowall\fR\ 'u
 \fBpepwindowall\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -37,8 +45,13 @@
 .PP
 \fB\-length\fR \fIinteger\fR
 .RS 4
-Default value: 7
+Default value: 19
 .RE
+.PP
+\fB\-normalize\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
 .SS "Output section"
 .PP
 \fB\-graph\fR \fIxygraph\fR
@@ -55,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/plotcon.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/plotcon.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/plotcon.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PLOTCON" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PLOTCON" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 plotcon \- Plot conservation of a sequence alignment
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBplotcon\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBplotcon\fR\ 'u
 \fBplotcon\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -55,11 +63,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/plotorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/plotorf.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/plotorf.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PLOTORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PLOTORF" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 plotorf \- Plot potential open reading frames in a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBplotorf\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBplotorf\fR\ 'u
 \fBplotorf\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/polydot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/polydot.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/polydot.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "POLYDOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "POLYDOT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-polydot \- Draw dotplots for all-against-all comparison of a sequence set
+polydot \- Draw dotplots for all\-against\-all comparison of a sequence set
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBpolydot\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBpolydot\fR\ 'u
 \fBpolydot\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/preg.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/preg.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/preg.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PREG" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PREG" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 preg \- Regular expression search of protein sequence(s)
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBpreg\fR\ 'u
 \fBpreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 5
+.HP \w'\fBpreg\fR\ 'u
 \fBpreg\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prettyplot.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRETTYPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRETTYPLOT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 11
+.HP \w'\fBprettyplot\fR\ 'u
+\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\-boxuse\ \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
+.HP \w'\fBprettyplot\fR\ 'u
 \fBprettyplot\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -93,7 +101,7 @@
 Default value: N
 .RE
 .PP
-\fB\-boxcolval\fR \fIstring\fR
+\fB\-boxuse\fR \fIstring\fR
 .RS 4
 Default value: GREY
 .RE
@@ -164,11 +172,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prettyseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRETTYSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRETTYSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 prettyseq \- Write a nucleotide sequence and its translation to file
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBprettyseq\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBprettyseq\fR\ 'u
 \fBprettyseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -75,11 +83,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prima.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prima.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prima.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRIMA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-prima \- Selects primers for PCR and DNA amplification.
+prima \- Selects primers for PCR and DNA amplification\&.
 .SH "SYNOPSIS"
-.HP 6
-\fBprima\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-targetrange\ \fR\fB\fItoggle\fR\fR \fB\-targetstart\ \fR\fB\fIinteger\fR\fR \fB\-targetend\ \fR\fB\fIinteger\fR\fR \fB\-minprimertm\ \fR\fB\fIfloat\fR\fR \fB\-maxprimertm\ \fR\fB\fIfloat\fR\fR \fB\-minprodlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprodlen\ \fR\fB\fIinteger\fR\fR \fB\-minprodgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxprodgccont\ \fR\fB\fIfloat\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-minprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-minpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-list\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 6
+.HP \w'\fBprima\fR\ 'u
+\fBprima\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-targetrange\ \fR\fB\fItoggle\fR\fR \fB\-targetstart\ \fR\fB\fIinteger\fR\fR \fB\-targetend\ \fR\fB\fIinteger\fR\fR \fB\-mintmprimer\ \fR\fB\fIfloat\fR\fR \fB\-maxtmprimer\ \fR\fB\fIfloat\fR\fR \fB\-minplen\ \fR\fB\fIinteger\fR\fR \fB\-maxplen\ \fR\fB\fIinteger\fR\fR \fB\-minpgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpgccont\ \fR\fB\fIfloat\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-minprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-minpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-list\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprima\fR\ 'u
 \fBprima\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -45,34 +53,34 @@
 Default value: $(sequence\&.length)
 .RE
 .PP
-\fB\-minprimertm\fR \fIfloat\fR
+\fB\-mintmprimer\fR \fIfloat\fR
 .RS 4
 Default value: 53
 .RE
 .PP
-\fB\-maxprimertm\fR \fIfloat\fR
+\fB\-maxtmprimer\fR \fIfloat\fR
 .RS 4
 Default value: 58
 .RE
 .SS "Additional section"
 .SS "Product options"
 .PP
-\fB\-minprodlen\fR \fIinteger\fR
+\fB\-minplen\fR \fIinteger\fR
 .RS 4
 Default value: 100
 .RE
 .PP
-\fB\-maxprodlen\fR \fIinteger\fR
+\fB\-maxplen\fR \fIinteger\fR
 .RS 4
 Default value: 300
 .RE
 .PP
-\fB\-minprodgccont\fR \fIfloat\fR
+\fB\-minpgccont\fR \fIfloat\fR
 .RS 4
 Default value: \&.40
 .RE
 .PP
-\fB\-maxprodgccont\fR \fIfloat\fR
+\fB\-maxpgccont\fR \fIfloat\fR
 .RS 4
 Default value: \&.55
 .RE
@@ -139,11 +147,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/primers.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/primers.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/primers.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRIMERS" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMERS" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 primers \- Simple version of primer3 to pick PCR primers
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBprimers\fR\ 'u
 \fBprimers\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-target\ \fR\fB\fIrange\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR] [\fB\-explainflag\ \fR\fB\fIboolean\fR\fR] [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 8
+.HP \w'\fBprimers\fR\ 'u
 \fBprimers\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -75,11 +83,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/primersearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/primersearch.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/primersearch.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRIMERSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRIMERSEARCH" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 primersearch \- Search DNA sequences for matches with primer pairs
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBprimersearch\fR\ 'u
 \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
-.HP 13
+.HP \w'\fBprimersearch\fR\ 'u
 \fBprimersearch\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -52,11 +60,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/printsextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/printsextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/printsextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PRINTSEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PRINTSEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 printsextract \- Extract data from PRINTS database for use by pscan
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBprintsextract\fR\ 'u
 \fBprintsextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
-.HP 14
+.HP \w'\fBprintsextract\fR\ 'u
 \fBprintsextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/profit.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/profit.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/profit.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PROFIT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PROFIT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 profit \- Scan one or more sequences with a simple frequency matrix
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBprofit\fR\ 'u
 \fBprofit\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 7
+.HP \w'\fBprofit\fR\ 'u
 \fBprofit\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prophecy.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prophecy.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prophecy.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PROPHECY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PROPHECY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 prophecy \- Create frequency matrix or profile from a multiple alignment
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBprophecy\fR\ 'u
 \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
-.HP 9
+.HP \w'\fBprophecy\fR\ 'u
 \fBprophecy\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -76,11 +84,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prophet.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prophet.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prophet.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PROPHET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PROPHET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 prophet \- Scan one or more sequences with a Gribskov or Henikoff profile
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBprophet\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBprophet\fR\ 'u
 \fBprophet\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -58,11 +66,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/prosextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/prosextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/prosextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PROSEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PROSEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 prosextract \- Processes the PROSITE motif database for use by patmatmotifs
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBprosextract\fR\ 'u
 \fBprosextract\fR \fB\-prositedir\ \fR\fB\fIdirectory\fR\fR
-.HP 12
+.HP \w'\fBprosextract\fR\ 'u
 \fBprosextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/pscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/pscan.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/pscan.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PSCAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 pscan \- Scans protein sequence(s) with fingerprints from the PRINTS database
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBpscan\fR\ 'u
 \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
-.HP 6
+.HP \w'\fBpscan\fR\ 'u
 \fBpscan\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/psiphi.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/psiphi.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/psiphi.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "PSIPHI" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "PSIPHI" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 psiphi \- Calculates phi and psi torsion angles from protein coordinates
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBpsiphi\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBpsiphi\fR\ 'u
 \fBpsiphi\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -60,11 +68,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/rebaseextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "REBASEEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "REBASEEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 rebaseextract \- Process the REBASE database for use by restriction enzyme applications
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBrebaseextract\fR\ 'u
 \fBrebaseextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-protofile\ \fR\fB\fIinfile\fR\fR [\fB\-equivalences\ \fR\fB\fIboolean\fR\fR]
-.HP 14
+.HP \w'\fBrebaseextract\fR\ 'u
 \fBrebaseextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/recoder.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/recoder.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/recoder.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "RECODER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "RECODER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 recoder \- Find restriction sites to remove (mutate) with no translation change
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBrecoder\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBrecoder\fR\ 'u
 \fBrecoder\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/redata.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/redata.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/redata.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "REDATA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "REDATA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 redata \- Retrieve information from REBASE restriction enzyme database
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBredata\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBredata\fR\ 'u
 \fBredata\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/remap.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/remap.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/remap.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "REMAP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "REMAP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 6
+.HP \w'\fBremap\fR\ 'u
+\fBremap\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\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\-methylation\ \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
+.HP \w'\fBremap\fR\ 'u
 \fBremap\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -27,6 +35,11 @@
 \fB\-sequence\fR \fIseqall\fR
 .RS 4
 .RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
 .SS "Required section"
 .PP
 \fB\-enzymes\fR \fIstring\fR
@@ -75,6 +88,11 @@
 If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered\&. Default value: N
 .RE
 .PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
 \fB\-commercial\fR \fIboolean\fR
 .RS 4
 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \'all\' the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
@@ -131,7 +149,7 @@
 .PP
 \fB\-highlight\fR \fIrange\fR
 .RS 4
-Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specifed as \'@filename\'\&.
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \'@filename\'\&.
 .RE
 .PP
 \fB\-threeletter\fR \fIboolean\fR
@@ -188,11 +206,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/restover.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/restover.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/restover.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "RESTOVER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "RESTOVER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 9
+.HP \w'\fBrestover\fR\ 'u
+\fBrestover\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \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\-methylation\ \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
+.HP \w'\fBrestover\fR\ 'u
 \fBrestover\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -31,6 +39,11 @@
 \fB\-datafile\fR \fIdatafile\fR
 .RS 4
 .RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
 .SS "Required section"
 .PP
 \fB\-seqcomp\fR \fIstring\fR
@@ -78,6 +91,11 @@
 Default value: N
 .RE
 .PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
 \fB\-commercial\fR \fIboolean\fR
 .RS 4
 Default value: Y
@@ -118,11 +136,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/restrict.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/restrict.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/restrict.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "RESTRICT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "RESTRICT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 9
+.HP \w'\fBrestrict\fR\ 'u
+\fBrestrict\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \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\-methylation\ \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
+.HP \w'\fBrestrict\fR\ 'u
 \fBrestrict\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -31,6 +39,11 @@
 \fB\-datafile\fR \fIdatafile\fR
 .RS 4
 .RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
 .SS "Required section"
 .PP
 \fB\-sitelen\fR \fIinteger\fR
@@ -84,6 +97,11 @@
 If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered\&. Default value: N
 .RE
 .PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
 \fB\-commercial\fR \fIboolean\fR
 .RS 4
 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \'all\' the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
@@ -124,11 +142,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/revseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/revseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/revseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "REVSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "REVSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 revseq \- Reverse and complement a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBrevseq\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBrevseq\fR\ 'u
 \fBrevseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -54,11 +62,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seealso.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seealso.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seealso.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEEALSO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEEALSO" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seealso \- Finds programs with similar function to a specified program
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBseealso\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBseealso\fR\ 'u
 \fBseealso\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -83,11 +91,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqinfo.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQINFO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQINFO" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqinfo \- Returns sequence information
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBseqinfo\fR\ 'u
 \fBseqinfo\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 8
+.HP \w'\fBseqinfo\fR\ 'u
 \fBseqinfo\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -44,11 +52,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqmatchall.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQMATCHALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQMATCHALL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-seqmatchall \- All-against-all word comparison of a sequence set
+seqmatchall \- All\-against\-all word comparison of a sequence set
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBseqmatchall\fR\ 'u
 \fBseqmatchall\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
-.HP 12
+.HP \w'\fBseqmatchall\fR\ 'u
 \fBseqmatchall\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqret.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqret.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqret.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqret \- Reads and writes (returns) sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBseqret\fR\ 'u
 \fBseqret\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
-.HP 7
+.HP \w'\fBseqret\fR\ 'u
 \fBseqret\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -53,11 +61,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqretall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretall.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretall.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETALL" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETALL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqretall \- Reads and writes (returns) a set of sequences one at a time
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBseqretall\fR\ 'u
 \fBseqretall\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 10
+.HP \w'\fBseqretall\fR\ 'u
 \fBseqretall\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretallfeat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETALLFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETALLFEAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqretallfeat \- Reads and writes (returns) one or more sequences
 .SH "SYNOPSIS"
-.HP 14
+.HP \w'\fBseqretallfeat\fR\ 'u
 \fBseqretallfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 14
+.HP \w'\fBseqretallfeat\fR\ 'u
 \fBseqretallfeat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -43,11 +51,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqretset.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretset.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretset.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETSET" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSET" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqretset \- Reads and writes (returns) a set of sequences all at once
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBseqretset\fR\ 'u
 \fBseqretset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR
-.HP 10
+.HP \w'\fBseqretset\fR\ 'u
 \fBseqretset\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Added: trunk/packages/emboss/trunk/debian/manpages/seqretsetall.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretsetall.1e	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretsetall.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: SEQRETSETALL
+.\"    Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
+.\"
+.TH "SEQRETSETALL" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretsetall \- Reads and writes (returns) many sets of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqretsetall\fR\ 'u
+\fBseqretsetall\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqretsetall\fR\ 'u
+\fBseqretsetall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretsetall\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 \fIseqsetall\fR
+.RS 4
+.RE
+.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
+seqretsetall 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\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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/seqretsingle.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretsingle.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETSINGLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSINGLE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqretsingle \- Reads and writes (returns) a single sequence
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBseqretsingle\fR\ 'u
 \fBseqretsingle\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
-.HP 13
+.HP \w'\fBseqretsingle\fR\ 'u
 \fBseqretsingle\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqretsplit.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETSPLIT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETSPLIT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqretsplit \- Reads sequences and writes them to individual files
 .SH "SYNOPSIS"
-.HP 12
+.HP \w'\fBseqretsplit\fR\ 'u
 \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
-.HP 12
+.HP \w'\fBseqretsplit\fR\ 'u
 \fBseqretsplit\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -52,11 +60,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/seqrettype.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SEQRETTYPE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SEQRETTYPE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 seqrettype \- Reads and writes (returns) sequences
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBseqrettype\fR\ 'u
 \fBseqrettype\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 11
+.HP \w'\fBseqrettype\fR\ 'u
 \fBseqrettype\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -57,11 +65,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/showalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showalign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/showalign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHOWALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 showalign \- Display a multiple sequence alignment in pretty format
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBshowalign\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBshowalign\fR\ 'u
 \fBshowalign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -136,11 +144,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/showdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showdb.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/showdb.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHOWDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWDB" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 showdb \- Displays information on configured databases
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBshowdb\fR\ 'u
 \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]
-.HP 7
+.HP \w'\fBshowdb\fR\ 'u
 \fBshowdb\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -121,11 +129,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/showfeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showfeat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/showfeat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHOWFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWFEAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 9
+.HP \w'\fBshowfeat\fR\ 'u
+\fBshowfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-sort\ \fR\fB\fIlist\fR\fR] [\fB\-joinfeatures\ \fR\fB\fIboolean\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\-origin\ \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
+.HP \w'\fBshowfeat\fR\ 'u
 \fBshowfeat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -29,22 +37,22 @@
 .RE
 .SS "Additional section"
 .PP
-\fB\-matchsource\fR \fIstring\fR
+\fB\-sourcematch\fR \fIstring\fR
 .RS 4
 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \'*\'\&. If you wish to show more than one source, separate their names with the character \'|\', eg: gene* | embl Default value: *
 .RE
 .PP
-\fB\-matchtype\fR \fIstring\fR
+\fB\-typematch\fR \fIstring\fR
 .RS 4
 By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www3\&.ebi\&.ac\&.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.ch/txt/userman\&.txt for a list of the Swissprot feature types\&. The type may be wildcarded by using \'*\'\&. If you wish to show more than one type, separate their names with the character \'|\', eg: *UTR | intron Default value: *
 .RE
 .PP
-\fB\-matchtag\fR \fIstring\fR
+\fB\-tagmatch\fR \fIstring\fR
 .RS 4
 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \'CDS\' type of feature may have the tags \'/codon\', \'/codon_start\', \'/db_xref\', \'/EC_number\', \'/evidence\', \'/exception\', \'/function\', \'/gene\', \'/label\', \'/map\', \'/note\', \'/number\', \'/partial\', \'/product\', \'/protein_id\', \'/pseudo\', \'/standard_name\', \'/translation\', \'/transl_except\', \'/transl_table\', or \'/usedin\'\&. Some of these tags also have values, for example \'/gene\' can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \'*\'\&. If you wish to show more than one tag, separate their names with the character \'|\', eg: gene | label Default value: *
 .RE
 .PP
-\fB\-matchvalue\fR \fIstring\fR
+\fB\-valuematch\fR \fIstring\fR
 .RS 4
 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \'CDS\' type of feature may have the tags \'/codon\', \'/codon_start\', \'/db_xref\', \'/EC_number\', \'/evidence\', \'/exception\', \'/function\', \'/gene\', \'/label\', \'/map\', \'/note\', \'/number\', \'/partial\', \'/product\', \'/protein_id\', \'/pseudo\', \'/standard_name\', \'/translation\', \'/transl_except\', \'/transl_table\', or \'/usedin\'\&. Only some of these tags can have values, for example \'/gene\' can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag valueyou wish to show\&. The tag value may be wildcarded by using \'*\'\&. If you wish to show more than one tag value, separate their names with the character \'|\', eg: pax* | 10 Default value: *
 .RE
@@ -54,6 +62,11 @@
 Default value: start
 .RE
 .PP
+\fB\-joinfeatures\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
 \fB\-annotation\fR \fIrange\fR
 .RS 4
 Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \'@filename\'\&.
@@ -110,9 +123,9 @@
 Set this if you wish to display the strand of the features\&. Protein features are always directionless (indicated by \'0\'), forward is indicated by \'+\' and reverse is \'\-\'\&. Default value: N
 .RE
 .PP
-\fB\-source\fR \fIboolean\fR
+\fB\-origin\fR \fIboolean\fR
 .RS 4
-Set this if you wish to display the source of the features\&. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from\&. Default value: N
+Set this if you wish to display the origin of the features\&. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from\&. Default value: N
 .RE
 .PP
 \fB\-position\fR \fIboolean\fR
@@ -155,11 +168,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/showorf.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showorf.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/showorf.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHOWORF" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWORF" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 showorf \- Display a nucleotide sequence and translation in pretty format
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBshoworf\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBshoworf\fR\ 'u
 \fBshoworf\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -74,11 +82,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Added: trunk/packages/emboss/trunk/debian/manpages/showpep.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showpep.1e	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/showpep.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -0,0 +1,169 @@
+'\" t
+.\"     Title: SHOWPEP
+.\"    Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
+.\"
+.TH "SHOWPEP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showpep \- Displays protein sequences with features in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshowpep\fR\ 'u
+\fBshowpep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\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
+.HP \w'\fBshowpep\fR\ 'u
+\fBshowpep\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowpep\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-format\fR \fIlist\fR
+.RS 4
+Default value: 2
+.RE
+.PP
+\fB\-things\fR \fIlist\fR
+.RS 4
+Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page\&. For example if you wish to see things displayed in the order: sequence, ticks line, blank line; then you should enter \'S,T,B\'\&. Default value: B,N,T,S,A,F
+.RE
+.SS "Additional section"
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \'@filename\'\&.
+.RE
+.PP
+\fB\-annotation\fR \fIrange\fR
+.RS 4
+Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \'@filename\'\&.
+.RE
+.SS "Feature display options"
+.PP
+\fB\-sourcematch\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \'*\'\&. If you wish to show more than one source, separate their names with the character \'|\', eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-typematch\fR \fIstring\fR
+.RS 4
+By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www3\&.ebi\&.ac\&.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.ch/txt/userman\&.txt for a list of the Swissprot feature types\&. The type may be wildcarded by using \'*\'\&. If you wish to show more than one type, separate their names with the character \'|\', eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum score of feature to display (see also maxscore) Default value: 0\&.0
+.RE
+.PP
+\fB\-maxscore\fR \fIfloat\fR
+.RS 4
+Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
+.RE
+.PP
+\fB\-tagmatch\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \'*\'\&. If you wish to show more than one tag, separate their names with the character \'|\', eg: gene | label Default value: *
+.RE
+.PP
+\fB\-valuematch\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag valueyou wish to show\&. The tag value may be wildcarded by using \'*\'\&. If you wish to show more than one tag value, separate their names with the character \'|\', eg: pax* | 10 Default value: *
+.RE
+.PP
+\fB\-stricttags\fR \fIboolean\fR
+.RS 4
+By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-threeletter\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence Default value: Y
+.RE
+.PP
+\fB\-offset\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.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
+showpep 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\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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/showseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/showseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/showseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHOWSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHOWSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 8
+.HP \w'\fBshowseq\fR\ 'u
+\fBshowseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-translate\ \fR\fB\fIrange\fR\fR] [\fB\-revtranslate\ \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\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-sensematch\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \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\-methylation\ \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
+.HP \w'\fBshowseq\fR\ 'u
 \fBshowseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -27,6 +35,11 @@
 \fB\-sequence\fR \fIseqall\fR
 .RS 4
 .RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
 .SS "Required section"
 .PP
 \fB\-format\fR \fIlist\fR
@@ -42,9 +55,14 @@
 .PP
 \fB\-translate\fR \fIrange\fR
 .RS 4
-Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888
 .RE
 .PP
+\fB\-revtranslate\fR \fIrange\fR
+.RS 4
+Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 78\-56, 45\-24, 888\&.\&.765, 99=67; 45:1
+.RE
+.PP
 \fB\-uppercase\fR \fIrange\fR
 .RS 4
 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
@@ -70,37 +88,37 @@
 .RE
 .SS "Feature display options"
 .PP
-\fB\-matchsource\fR \fIstring\fR
+\fB\-sourcematch\fR \fIstring\fR
 .RS 4
 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \'*\'\&. If you wish to show more than one source, separate their names with the character \'|\', eg: gene* | embl Default value: *
 .RE
 .PP
-\fB\-matchtype\fR \fIstring\fR
+\fB\-typematch\fR \fIstring\fR
 .RS 4
 By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www3\&.ebi\&.ac\&.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.ch/txt/userman\&.txt for a list of the Swissprot feature types\&. The type may be wildcarded by using \'*\'\&. If you wish to show more than one type, separate their names with the character \'|\', eg: *UTR | intron Default value: *
 .RE
 .PP
-\fB\-matchsense\fR \fIinteger\fR
+\fB\-sensematch\fR \fIinteger\fR
 .RS 4
 By default any feature type in the feature table is shown\&. You can set this to match any feature sense you wish to show\&. 0 \- any sense, 1 \- forward sense, \-1 \- reverse sense
 .RE
 .PP
 \fB\-minscore\fR \fIfloat\fR
 .RS 4
-If this is greater than or equal to the maximum score, then any score is permitted Default value: 0\&.0
+Minimum score of feature to display (see also maxscore) Default value: 0\&.0
 .RE
 .PP
 \fB\-maxscore\fR \fIfloat\fR
 .RS 4
-If this is less than or equal to the maximum score, then any score is permitted Default value: 0\&.0
+Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
 .RE
 .PP
-\fB\-matchtag\fR \fIstring\fR
+\fB\-tagmatch\fR \fIstring\fR
 .RS 4
 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \'CDS\' type of feature may have the tags \'/codon\', \'/codon_start\', \'/db_xref\', \'/EC_number\', \'/evidence\', \'/exception\', \'/function\', \'/gene\', \'/label\', \'/map\', \'/note\', \'/number\', \'/partial\', \'/product\', \'/protein_id\', \'/pseudo\', \'/standard_name\', \'/translation\', \'/transl_except\', \'/transl_table\', or \'/usedin\'\&. Some of these tags also have values, for example \'/gene\' can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \'*\'\&. If you wish to show more than one tag, separate their names with the character \'|\', eg: gene | label Default value: *
 .RE
 .PP
-\fB\-matchvalue\fR \fIstring\fR
+\fB\-valuematch\fR \fIstring\fR
 .RS 4
 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \'CDS\' type of feature may have the tags \'/codon\', \'/codon_start\', \'/db_xref\', \'/EC_number\', \'/evidence\', \'/exception\', \'/function\', \'/gene\', \'/label\', \'/map\', \'/note\', \'/number\', \'/partial\', \'/product\', \'/protein_id\', \'/pseudo\', \'/standard_name\', \'/translation\', \'/transl_except\', \'/transl_table\', or \'/usedin\'\&. Only some of these tags can have values, for example \'/gene\' can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag valueyou wish to show\&. The tag value may be wildcarded by using \'*\'\&. If you wish to show more than one tag value, separate their names with the character \'|\', eg: pax* | 10 Default value: *
 .RE
@@ -157,6 +175,11 @@
 If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered\&. Default value: N
 .RE
 .PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
 \fB\-commercial\fR \fIboolean\fR
 .RS 4
 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \'all\' the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
@@ -231,11 +254,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/shuffleseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SHUFFLESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SHUFFLESEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 shuffleseq \- Shuffles a set of sequences maintaining composition
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBshuffleseq\fR\ 'u
 \fBshuffleseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 11
+.HP \w'\fBshuffleseq\fR\ 'u
 \fBshuffleseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/sigcleave.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SIGCLEAVE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SIGCLEAVE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 sigcleave \- Reports on signal cleavage sites in a protein sequence
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBsigcleave\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBsigcleave\fR\ 'u
 \fBsigcleave\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -55,11 +63,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/silent.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/silent.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/silent.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SILENT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SILENT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 silent \- Find restriction sites to insert (mutate) with no translation change
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBsilent\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBsilent\fR\ 'u
 \fBsilent\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -64,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/sirna.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sirna.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/sirna.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SIRNA" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SIRNA" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 sirna \- Finds siRNA duplexes in mRNA
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBsirna\fR\ 'u
 \fBsirna\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-poliii\ \fR\fB\fIboolean\fR\fR] [\fB\-aa\ \fR\fB\fIboolean\fR\fR] [\fB\-tt\ \fR\fB\fIboolean\fR\fR] [\fB\-polybase\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-context\ \fR\fB\fIboolean\fR\fR]
-.HP 6
+.HP \w'\fBsirna\fR\ 'u
 \fBsirna\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -75,11 +83,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/sixpack.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sixpack.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/sixpack.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SIXPACK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SIXPACK" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-sixpack \- Display a DNA sequence with 6-frame translation and ORFs
+sixpack \- Display a DNA sequence with 6\-frame translation and ORFs
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBsixpack\fR\ 'u
 \fBsixpack\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-firstorf\ \fR\fB\fIboolean\fR\fR] [\fB\-lastorf\ \fR\fB\fIboolean\fR\fR] [\fB\-mstart\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\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\-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
-.HP 8
+.HP \w'\fBsixpack\fR\ 'u
 \fBsixpack\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -76,7 +84,7 @@
 .PP
 \fB\-highlight\fR \fIrange\fR
 .RS 4
-Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specifed as \'@filename\'\&.
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \'@filename\'\&.
 .RE
 .PP
 \fB\-number\fR \fIboolean\fR
@@ -128,11 +136,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/sizeseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SIZESEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SIZESEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 sizeseq \- Sort sequences by size
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBsizeseq\fR\ 'u
 \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
+.HP \w'\fBsizeseq\fR\ 'u
 \fBsizeseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -56,11 +64,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/skipredundant.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SKIPREDUNDANT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SKIPREDUNDANT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .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
+.HP \w'\fBskipredundant\fR\ 'u
+\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\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-redundantoutseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBskipredundant\fR\ 'u
 \fBskipredundant\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,6 @@
 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
@@ -94,11 +97,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/skipseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/skipseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/skipseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SKIPSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SKIPSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 skipseq \- Reads and writes (returns) sequences, skipping first few
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBskipseq\fR\ 'u
 \fBskipseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-skip\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 8
+.HP \w'\fBskipseq\fR\ 'u
 \fBskipseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -51,11 +59,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Added: trunk/packages/emboss/trunk/debian/manpages/splitsource.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/splitsource.1e	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/manpages/splitsource.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -0,0 +1,68 @@
+'\" t
+.\"     Title: SPLITSOURCE
+.\"    Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
+.\"
+.TH "SPLITSOURCE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+splitsource \- Split sequence(s) into original source sequences
+.SH "SYNOPSIS"
+.HP \w'\fBsplitsource\fR\ 'u
+\fBsplitsource\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBsplitsource\fR\ 'u
+\fBsplitsource\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsplitsource\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
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.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
+splitsource 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\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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/splitter.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/splitter.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/splitter.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SPLITTER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SPLITTER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 9
+.HP \w'\fBsplitter\fR\ 'u
+\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\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBsplitter\fR\ 'u
 \fBsplitter\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -42,16 +50,6 @@
 \fB\-overlap\fR \fIinteger\fR
 .RS 4
 .RE
-.PP
-\fB\-source\fR \fIboolean\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-multifile\fR \fIboolean\fR
-.RS 4
-Default value: N
-.RE
 .SS "Advanced section"
 .PP
 \fB\-addoverlap\fR \fIboolean\fR
@@ -74,11 +72,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/stretcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/stretcher.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/stretcher.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "STRETCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "STRETCHER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-stretcher \- Needleman-Wunsch rapid global alignment of two sequences
+stretcher \- Needleman\-Wunsch rapid global alignment of two sequences
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBstretcher\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBstretcher\fR\ 'u
 \fBstretcher\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/stssearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/stssearch.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/stssearch.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "STSSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "STSSEARCH" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 stssearch \- Search a DNA database for matches with a set of STS primers
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBstssearch\fR\ 'u
 \fBstssearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBstssearch\fR\ 'u
 \fBstssearch\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -47,11 +55,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/supermatcher.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SUPERMATCHER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SUPERMATCHER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-supermatcher \- Calculate approximate local pair-wise alignments of larger sequences
+supermatcher \- Calculate approximate local pair\-wise alignments of larger sequences
 .SH "SYNOPSIS"
-.HP 13
+.HP \w'\fBsupermatcher\fR\ 'u
 \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]
-.HP 13
+.HP \w'\fBsupermatcher\fR\ 'u
 \fBsupermatcher\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -79,11 +87,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/syco.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/syco.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/syco.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "SYCO" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "SYCO" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 syco \- Draw synonymous codon usage statictic plot for a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBsyco\fR\ 'u
 \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
-.HP 5
+.HP \w'\fBsyco\fR\ 'u
 \fBsyco\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -73,11 +81,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tcode.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tcode.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tcode.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TCODE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TCODE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-tcode \- Identify protein-coding regions using Fickett TESTCODE statistic
+tcode \- Identify protein\-coding regions using Fickett TESTCODE statistic
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBtcode\fR\ 'u
 \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
-.HP 6
+.HP \w'\fBtcode\fR\ 'u
 \fBtcode\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -69,11 +77,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/testplot.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/testplot.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/testplot.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TESTPLOT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TESTPLOT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 testplot \- Test plot
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBtestplot\fR\ 'u
 \fBtestplot\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
-.HP 9
+.HP \w'\fBtestplot\fR\ 'u
 \fBtestplot\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -49,11 +57,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/textsearch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/textsearch.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/textsearch.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TEXTSEARCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TEXTSEARCH" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 textsearch \- Search the textual description of sequence(s)
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBtextsearch\fR\ 'u
 \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
-.HP 11
+.HP \w'\fBtextsearch\fR\ 'u
 \fBtextsearch\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -90,11 +98,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tfextract.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfextract.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tfextract.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TFEXTRACT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TFEXTRACT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 tfextract \- Process TRANSFAC transcription factor database for use by tfscan
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBtfextract\fR\ 'u
 \fBtfextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
-.HP 10
+.HP \w'\fBtfextract\fR\ 'u
 \fBtfextract\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tfm.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfm.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tfm.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TFM" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TFM" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 tfm \- Displays full documentation for an application
 .SH "SYNOPSIS"
-.HP 4
+.HP \w'\fBtfm\fR\ 'u
 \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]
-.HP 4
+.HP \w'\fBtfm\fR\ 'u
 \fBtfm\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -55,11 +63,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tfscan.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tfscan.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tfscan.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TFSCAN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TFSCAN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 tfscan \- Identify transcription factor binding sites in DNA sequences
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBtfscan\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBtfscan\fR\ 'u
 \fBtfscan\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tmap.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tmap.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tmap.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TMAP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TMAP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 tmap \- Predict and plot transmembrane segments in protein sequences
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fBtmap\fR\ 'u
 \fBtmap\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
-.HP 5
+.HP \w'\fBtmap\fR\ 'u
 \fBtmap\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/tranalign.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/tranalign.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/tranalign.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TRANALIGN" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TRANALIGN" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-tranalign \- Generate an aligment of nucleic coding regions from aligned proteins
+tranalign \- Generate an alignment of nucleic coding regions from aligned proteins
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBtranalign\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBtranalign\fR\ 'u
 \fBtranalign\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -52,11 +60,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/transeq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/transeq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/transeq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TRANSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TRANSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 transeq \- Translate nucleic acid sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBtranseq\fR\ 'u
 \fBtranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-regions\ \fR\fB\fIrange\fR\fR] [\fB\-trim\ \fR\fB\fIboolean\fR\fR] [\fB\-clean\ \fR\fB\fIboolean\fR\fR] \fB\-alternative\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
-.HP 8
+.HP \w'\fBtranseq\fR\ 'u
 \fBtranseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -74,11 +82,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/treetypedisplay.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TREETYPEDISPLAY" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TREETYPEDISPLAY" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 treetypedisplay \- Test of graphics
 .SH "SYNOPSIS"
-.HP 16
+.HP \w'\fBtreetypedisplay\fR\ 'u
 \fBtreetypedisplay\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
-.HP 16
+.HP \w'\fBtreetypedisplay\fR\ 'u
 \fBtreetypedisplay\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -38,11 +46,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/trimest.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimest.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/trimest.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TRIMEST" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TRIMEST" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-trimest \- Remove poly-A tails from nucleotide sequences
+trimest \- Remove poly\-A tails from nucleotide sequences
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBtrimest\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBtrimest\fR\ 'u
 \fBtrimest\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -70,11 +78,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/trimseq.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimseq.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/trimseq.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TRIMSEQ" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TRIMSEQ" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 trimseq \- Remove unwanted characters from start and end of sequence(s)
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBtrimseq\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBtrimseq\fR\ 'u
 \fBtrimseq\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -75,11 +83,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/trimspace.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/trimspace.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/trimspace.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TRIMSPACE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TRIMSPACE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 trimspace \- Remove extra whitespace from an ASCII text file
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBtrimspace\fR\ 'u
 \fBtrimspace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 10
+.HP \w'\fBtrimspace\fR\ 'u
 \fBtrimspace\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -46,11 +54,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/twofeat.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/twofeat.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/twofeat.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "TWOFEAT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "TWOFEAT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 twofeat \- Finds neighbouring pairs of features in sequence(s)
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBtwofeat\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBtwofeat\fR\ 'u
 \fBtwofeat\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -156,11 +164,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/union.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/union.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/union.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "UNION" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "UNION" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 union \- Concatenate multiple sequences into a single sequence
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBunion\fR\ 'u
 \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]
-.HP 6
+.HP \w'\fBunion\fR\ 'u
 \fBunion\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -63,11 +71,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/vectorstrip.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "VECTORSTRIP" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "VECTORSTRIP" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 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
-.HP 12
+.HP \w'\fBvectorstrip\fR\ 'u
+\fBvectorstrip\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-readfile\ \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\-alinker\ \fR\fB\fIstring\fR\fR \fB\-blinker\ \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
+.HP \w'\fBvectorstrip\fR\ 'u
 \fBvectorstrip\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -29,7 +37,7 @@
 .RE
 .SS "Vector input options"
 .PP
-\fB\-vectorfile\fR \fItoggle\fR
+\fB\-readfile\fR \fItoggle\fR
 .RS 4
 Default value: Y
 .RE
@@ -49,11 +57,11 @@
 Default value: Y
 .RE
 .PP
-\fB\-linkera\fR \fIstring\fR
+\fB\-alinker\fR \fIstring\fR
 .RS 4
 .RE
 .PP
-\fB\-linkerb\fR \fIstring\fR
+\fB\-blinker\fR \fIstring\fR
 .RS 4
 .RE
 .SS "Output section"
@@ -81,11 +89,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/water.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/water.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/water.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WATER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WATER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
-water \- Smith-Waterman local alignment of sequences
+water \- Smith\-Waterman local alignment of sequences
 .SH "SYNOPSIS"
-.HP 6
+.HP \w'\fBwater\fR\ 'u
 \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
-.HP 6
+.HP \w'\fBwater\fR\ 'u
 \fBwater\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -68,11 +76,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/whichdb.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/whichdb.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/whichdb.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WHICHDB" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WHICHDB" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 whichdb \- Search all sequence databases for an entry and retrieve it
 .SH "SYNOPSIS"
-.HP 8
+.HP \w'\fBwhichdb\fR\ 'u
 \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
-.HP 8
+.HP \w'\fBwhichdb\fR\ 'u
 \fBwhichdb\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -53,11 +61,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/wobble.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wobble.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/wobble.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WOBBLE" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WOBBLE" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 wobble \- Plot third base position variability in a nucleotide sequence
 .SH "SYNOPSIS"
-.HP 7
+.HP \w'\fBwobble\fR\ 'u
 \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
-.HP 7
+.HP \w'\fBwobble\fR\ 'u
 \fBwobble\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -59,11 +67,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/wordcount.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordcount.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/wordcount.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,26 +1,34 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WORDCOUNT" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WORDCOUNT" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 wordcount \- Count and extract unique words in DNA sequence(s)
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBwordcount\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBwordcount\fR\ 'u
 \fBwordcount\fR \fB\-help\fR
 .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,Protein: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
@@ -55,11 +63,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/wordfinder.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WORDFINDER" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WORDFINDER" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 wordfinder \- Match large sequences against one or more other sequences
 .SH "SYNOPSIS"
-.HP 11
+.HP \w'\fBwordfinder\fR\ 'u
 \fBwordfinder\fR \fB\-asequence\ \fR\fB\fIseqset\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\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] [\fB\-limitmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-limitalign\ \fR\fB\fIinteger\fR\fR] [\fB\-lowmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-lowalign\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
-.HP 11
+.HP \w'\fBwordfinder\fR\ 'u
 \fBwordfinder\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -95,11 +103,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/wordmatch.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WORDMATCH" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WORDMATCH" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 wordmatch \- Finds regions of identity (exact matches) of two sequences
 .SH "SYNOPSIS"
-.HP 10
+.HP \w'\fBwordmatch\fR\ 'u
 \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
-.HP 10
+.HP \w'\fBwordmatch\fR\ 'u
 \fBwordmatch\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -61,11 +69,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/wossname.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/wossname.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/wossname.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "WOSSNAME" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "WOSSNAME" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 wossname \- Finds programs by keywords in their short description
 .SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBwossname\fR\ 'u
 \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]
-.HP 9
+.HP \w'\fBwossname\fR\ 'u
 \fBwossname\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -103,11 +111,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.

Modified: trunk/packages/emboss/trunk/debian/manpages/yank.1e
===================================================================
--- trunk/packages/emboss/trunk/debian/manpages/yank.1e	2009-07-15 12:35:17 UTC (rev 3638)
+++ trunk/packages/emboss/trunk/debian/manpages/yank.1e	2009-07-15 13:10:24 UTC (rev 3639)
@@ -1,21 +1,29 @@
+'\" t
 .\"     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: 07/16/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\"      Date: 07/15/2009
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 6.0.0
+.\"    Source: EMBOSS 6.1.0
+.\"  Language: English
 .\"
-.TH "YANK" "1e" "07/16/2008" "EMBOSS 6.0.0" "EMBOSS Manual for Debian"
+.TH "YANK" "1e" "07/15/2009" "EMBOSS 6.1.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
 .SH "NAME"
 yank \- Add a sequence reference (a full USA) to a list file
 .SH "SYNOPSIS"
-.HP 5
+.HP \w'\fByank\fR\ 'u
 \fByank\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-newfile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP 5
+.HP \w'\fByank\fR\ 'u
 \fByank\fR \fB\-help\fR
 .SH "DESCRIPTION"
 .PP
@@ -48,11 +56,10 @@
 .SH "AUTHOR"
 .PP
 \fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
 Wrote the script used to autogenerate this manual page\&.
+.RE
 .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\&.


