[med-svn] r3732 - in trunk/packages/embassy-phylip/trunk/debian: . manpages
Charles Plessy
plessy at alioth.debian.org
Tue Aug 4 13:17:35 UTC 2009
Author: plessy
Date: 2009-08-04 13:17:35 +0000 (Tue, 04 Aug 2009)
New Revision: 3732
Added:
trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.manpages
trunk/packages/embassy-phylip/trunk/debian/manpages/
trunk/packages/embassy-phylip/trunk/debian/manpages/fclique.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fconsense.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fcontml.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fcontrast.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdiscboot.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnacomp.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnadist.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnainvar.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnaml.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamlk.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamove.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapars.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapenny.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdollop.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdolmove.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdolpenny.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawgram.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawtree.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/ffactor.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/ffitch.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/ffreqboot.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fgendist.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fkitsch.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fmix.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fmove.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fneighbor.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fpars.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fpenny.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fproml.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fpromlk.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fprotdist.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fprotpars.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/frestboot.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/frestdist.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/frestml.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fretree.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fseqboot.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/fseqbootall.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedist.1e
trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedistpair.1e
Log:
Created manpages with build-manpages.sh (from the emboss directory).
Added: trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.manpages
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.manpages (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.manpages 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,40 @@
+debian/manpages/fretree.1e
+debian/manpages/fprotpars.1e
+debian/manpages/fpromlk.1e
+debian/manpages/fdollop.1e
+debian/manpages/frestml.1e
+debian/manpages/ftreedistpair.1e
+debian/manpages/fdrawtree.1e
+debian/manpages/frestdist.1e
+debian/manpages/fkitsch.1e
+debian/manpages/fdnapenny.1e
+debian/manpages/fdnapars.1e
+debian/manpages/fdnainvar.1e
+debian/manpages/fmix.1e
+debian/manpages/fpars.1e
+debian/manpages/fprotdist.1e
+debian/manpages/fpenny.1e
+debian/manpages/ffreqboot.1e
+debian/manpages/frestboot.1e
+debian/manpages/fdrawgram.1e
+debian/manpages/fdiscboot.1e
+debian/manpages/fconsense.1e
+debian/manpages/fmove.1e
+debian/manpages/fneighbor.1e
+debian/manpages/fdnaml.1e
+debian/manpages/fdolmove.1e
+debian/manpages/fdnacomp.1e
+debian/manpages/fdnamlk.1e
+debian/manpages/fproml.1e
+debian/manpages/fclique.1e
+debian/manpages/fcontml.1e
+debian/manpages/fdnamove.1e
+debian/manpages/ftreedist.1e
+debian/manpages/fgendist.1e
+debian/manpages/fseqboot.1e
+debian/manpages/fdnadist.1e
+debian/manpages/fcontrast.1e
+debian/manpages/ffitch.1e
+debian/manpages/fseqbootall.1e
+debian/manpages/ffactor.1e
+debian/manpages/fdolpenny.1e
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fclique.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fclique.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fclique.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,111 @@
+'\" t
+.\" Title: FCLIQUE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FCLIQUE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fclique \- Largest clique program
+.SH "SYNOPSIS"
+.HP \w'\fBfclique\fR\ 'u
+\fBfclique\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-cliqmin\ \fR\fB\fIinteger\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-printcomp\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfclique\fR\ 'u
+\fBfclique\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfclique\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-factorfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-cliqmin\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-printcomp\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fclique 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fconsense.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fconsense.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fconsense.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,105 @@
+'\" t
+.\" Title: FCONSENSE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FCONSENSE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fconsense \- Majority\-rule and strict consensus tree
+.SH "SYNOPSIS"
+.HP \w'\fBfconsense\fR\ 'u
+\fBfconsense\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-mlfrac\ \fR\fB\fIfloat\fR\fR [\fB\-root\ \fR\fB\fItoggle\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-prntsets\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfconsense\fR\ 'u
+\fBfconsense\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfconsense\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: mre
+.RE
+.PP
+\fB\-mlfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.5
+.RE
+.PP
+\fB\-root\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-prntsets\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fconsense 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fcontml.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fcontml.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fcontml.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,119 @@
+'\" t
+.\" Title: FCONTML
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FCONTML" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fcontml \- Gene frequency and continuous character Maximum Likelihood
+.SH "SYNOPSIS"
+.HP \w'\fBfcontml\fR\ 'u
+\fBfcontml\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-datatype\ \fR\fB\fIlist\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfcontml\fR\ 'u
+\fBfcontml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfcontml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIfrequencies\fR
+.RS 4
+File containing one or more sets of data
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-datatype\fR \fIlist\fR
+.RS 4
+Default value: g
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fcontml 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fcontrast.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fcontrast.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fcontrast.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,97 @@
+'\" t
+.\" Title: FCONTRAST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FCONTRAST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fcontrast \- Continuous character Contrasts
+.SH "SYNOPSIS"
+.HP \w'\fBfcontrast\fR\ 'u
+\fBfcontrast\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-varywithin\ \fR\fB\fIboolean\fR\fR] \fB\-reg\ \fR\fB\fIboolean\fR\fR \fB\-writecont\ \fR\fB\fIboolean\fR\fR \fB\-nophylo\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfcontrast\fR\ 'u
+\fBfcontrast\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfcontrast\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Continuous characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIfrequencies\fR
+.RS 4
+File containing one or more sets of data
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-varywithin\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-reg\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-writecont\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-nophylo\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fcontrast 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdiscboot.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdiscboot.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdiscboot.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,146 @@
+'\" t
+.\" Title: FDISCBOOT
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDISCBOOT" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdiscboot \- Bootstrapped discrete sites algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfdiscboot\fR\ 'u
+\fBfdiscboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR \fB\-outmixfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdiscboot\fR\ 'u
+\fBfdiscboot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdiscboot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+.RE
+.PP
+\fB\-mixfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.PP
+\fB\-factorfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-test\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-regular\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fracsample\fR \fIfloat\fR
+.RS 4
+Default value: 100\&.0
+.RE
+.PP
+\fB\-morphseqtype\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-blocksize\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-reps\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-justweights\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outancfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outmixfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outfactfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fdiscboot 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnacomp.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnacomp.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnacomp.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,118 @@
+'\" t
+.\" Title: FDNACOMP
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNACOMP" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnacomp \- DNA compatibility algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfdnacomp\fR\ 'u
+\fBfdnacomp\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnacomp\fR\ 'u
+\fBfdnacomp\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnacomp\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdnacomp 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnadist.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnadist.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnadist.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,137 @@
+'\" t
+.\" Title: FDNADIST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNADIST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnadist \- Nucleic acid sequence Distance Matrix program
+.SH "SYNOPSIS"
+.HP \w'\fBfdnadist\fR\ 'u
+\fBfdnadist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-ncategories\ \fR\fB\fIinteger\fR\fR \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-lower\ \fR\fB\fIboolean\fR\fR] [\fB\-humanreadable\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnadist\fR\ 'u
+\fBfdnadist\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnadist\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: F84 distance model
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: No distribution parameters used
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+File of substitution rate categories
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-ttratio\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-freqsfrom\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-basefreq\fR \fIarray\fR
+.RS 4
+Default value: 0\&.25 0\&.25 0\&.25 0\&.25
+.RE
+.PP
+\fB\-lower\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-humanreadable\fR \fIboolean\fR
+.RS 4
+Default value: @($(method)==s?Y:N)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fdnadist 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnainvar.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnainvar.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnainvar.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,91 @@
+'\" t
+.\" Title: FDNAINVAR
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAINVAR" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnainvar \- Nucleic acid sequence Invariants method
+.SH "SYNOPSIS"
+.HP \w'\fBfdnainvar\fR\ 'u
+\fBfdnainvar\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-printpattern\ \fR\fB\fIboolean\fR\fR] [\fB\-printinvariant\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnainvar\fR\ 'u
+\fBfdnainvar\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnainvar\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-printpattern\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-printinvariant\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fdnainvar 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnaml.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnaml.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnaml.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,212 @@
+'\" t
+.\" Title: FDNAML
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAML" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnaml \- Estimates nucleotide phylogeny by maximum likelihood
+.SH "SYNOPSIS"
+.HP \w'\fBfdnaml\fR\ 'u
+\fBfdnaml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnaml\fR\ 'u
+\fBfdnaml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnaml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.SS "Additional section"
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ttratio\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-freqsfrom\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-basefreq\fR \fIarray\fR
+.RS 4
+Default value: 0\&.25 0\&.25 0\&.25 0\&.25
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: Constant rate
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ngammacat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarcoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ninvarcat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-nhmmcategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hmmrates\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-hmmprobabilities\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-adjsite\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-lambda\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-rough\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-hypstate\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdnaml 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamlk.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamlk.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamlk.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,202 @@
+'\" t
+.\" Title: FDNAMLK
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAMLK" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnamlk \- Estimates nucleotide phylogeny by maximum likelihood
+.SH "SYNOPSIS"
+.HP \w'\fBfdnamlk\fR\ 'u
+\fBfdnamlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnamlk\fR\ 'u
+\fBfdnamlk\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnamlk\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-ttratio\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-freqsfrom\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-basefreq\fR \fIarray\fR
+.RS 4
+Default value: 0\&.25 0\&.25 0\&.25 0\&.25
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: Constant rate
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ngammacat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarcoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ninvarcat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-nhmmcategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hmmrates\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-hmmprobabilities\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-adjsite\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-lambda\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-hypstate\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdnamlk 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamove.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamove.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnamove.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,100 @@
+'\" t
+.\" Title: FDNAMOVE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAMOVE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnamove \- Interactive DNA parsimony
+.SH "SYNOPSIS"
+.HP \w'\fBfdnamove\fR\ 'u
+\fBfdnamove\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBfdnamove\fR\ 'u
+\fBfdnamove\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnamove\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file \- ignore sites with weight zero
+.RE
+.SS "Additional section"
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-initialtree\fR \fIlist\fR
+.RS 4
+Default value: Arbitary
+.RE
+.PP
+\fB\-screenwidth\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-screenlines\fR \fIinteger\fR
+.RS 4
+Default value: 24
+.RE
+.SS "Output section"
+.PP
+\fB\-outtreefile\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
+fdnamove 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapars.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapars.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapars.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,153 @@
+'\" t
+.\" Title: FDNAPARS
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAPARS" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnapars \- DNA parsimony algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfdnapars\fR\ 'u
+\fBfdnapars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR [\fB\-transversion\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBfdnapars\fR\ 'u
+\fBfdnapars\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnapars\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-maxtrees\fR \fIinteger\fR
+.RS 4
+Default value: 10000
+.RE
+.PP
+\fB\-thorough\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-rearrange\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-transversion\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fdnapars 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapenny.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapenny.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdnapenny.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,130 @@
+'\" t
+.\" Title: FDNAPENNY
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDNAPENNY" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdnapenny \- Penny algorithm for DNA
+.SH "SYNOPSIS"
+.HP \w'\fBfdnapenny\fR\ 'u
+\fBfdnapenny\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdnapenny\fR\ 'u
+\fBfdnapenny\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdnapenny\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-howoften\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-howmany\fR \fIinteger\fR
+.RS 4
+Default value: 1000
+.RE
+.PP
+\fB\-simple\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdnapenny 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdollop.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdollop.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdollop.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,128 @@
+'\" t
+.\" Title: FDOLLOP
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDOLLOP" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdollop \- Dollo and polymorphism parsimony algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfdollop\fR\ 'u
+\fBfdollop\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdollop\fR\ 'u
+\fBfdollop\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdollop\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more data sets
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: $(infile\&.discretesize)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdollop 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdolmove.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdolmove.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdolmove.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,110 @@
+'\" t
+.\" Title: FDOLMOVE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDOLMOVE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdolmove \- Interactive Dollo or Polymorphism Parsimony
+.SH "SYNOPSIS"
+.HP \w'\fBfdolmove\fR\ 'u
+\fBfdolmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBfdolmove\fR\ 'u
+\fBfdolmove\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdolmove\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing data set
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-factorfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-initialtree\fR \fIlist\fR
+.RS 4
+Default value: Arbitary
+.RE
+.PP
+\fB\-screenwidth\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-screenlines\fR \fIinteger\fR
+.RS 4
+Default value: 24
+.RE
+.SS "Output section"
+.PP
+\fB\-outtreefile\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
+fdolmove 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdolpenny.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdolpenny.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdolpenny.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,135 @@
+'\" t
+.\" Title: FDOLPENNY
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDOLPENNY" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdolpenny \- Penny algorithm Dollo or polymorphism
+.SH "SYNOPSIS"
+.HP \w'\fBfdolpenny\fR\ 'u
+\fBfdolpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfdolpenny\fR\ 'u
+\fBfdolpenny\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdolpenny\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more data sets
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-howmany\fR \fIinteger\fR
+.RS 4
+Default value: 1000
+.RE
+.PP
+\fB\-howoften\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-simple\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fdolpenny 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawgram.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawgram.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawgram.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,177 @@
+'\" t
+.\" Title: FDRAWGRAM
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDRAWGRAM" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdrawgram \- Plots a cladogram\- or phenogram\-like rooted tree diagram
+.SH "SYNOPSIS"
+.HP \w'\fBfdrawgram\fR\ 'u
+\fBfdrawgram\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-grows\ \fR\fB\fIboolean\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] [\fB\-stemlength\ \fR\fB\fIfloat\fR\fR] [\fB\-nodespace\ \fR\fB\fIfloat\fR\fR] [\fB\-nodeposition\ \fR\fB\fIlist\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR]
+.HP \w'\fBfdrawgram\fR\ 'u
+\fBfdrawgram\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdrawgram\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-fontfile\fR \fIstring\fR
+.RS 4
+Default value: font1
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Output section"
+.PP
+\fB\-plotfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-grows\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-style\fR \fIlist\fR
+.RS 4
+Default value: c
+.RE
+.PP
+\fB\-plotter\fR \fIlist\fR
+.RS 4
+Default value: l
+.RE
+.PP
+\fB\-previewer\fR \fIlist\fR
+.RS 4
+Default value: x
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-labelrotation\fR \fIfloat\fR
+.RS 4
+Default value: 90\&.0
+.RE
+.PP
+\fB\-rescaled\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-bscale\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-treedepth\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.53
+.RE
+.PP
+\fB\-stemlength\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.05
+.RE
+.PP
+\fB\-nodespace\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.3333
+.RE
+.PP
+\fB\-nodeposition\fR \fIlist\fR
+.RS 4
+Default value: c
+.RE
+.PP
+\fB\-xmargin\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.65
+.RE
+.PP
+\fB\-ymargin\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.16
+.RE
+.PP
+\fB\-xrayshade\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.65
+.RE
+.PP
+\fB\-yrayshade\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.16
+.RE
+.PP
+\fB\-paperx\fR \fIfloat\fR
+.RS 4
+Default value: 20\&.63750
+.RE
+.PP
+\fB\-papery\fR \fIfloat\fR
+.RS 4
+Default value: 26\&.98750
+.RE
+.PP
+\fB\-pagesheight\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-pageswidth\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hpmargin\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.41275
+.RE
+.PP
+\fB\-vpmargin\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.53975
+.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
+fdrawgram 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawtree.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawtree.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fdrawtree.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,172 @@
+'\" t
+.\" Title: FDRAWTREE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FDRAWTREE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fdrawtree \- Plots an unrooted tree diagram
+.SH "SYNOPSIS"
+.HP \w'\fBfdrawtree\fR\ 'u
+\fBfdrawtree\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-iterate\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] [\fB\-labeldirection\ \fR\fB\fIlist\fR\fR] [\fB\-treeangle\ \fR\fB\fIfloat\fR\fR] [\fB\-arc\ \fR\fB\fIfloat\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR]
+.HP \w'\fBfdrawtree\fR\ 'u
+\fBfdrawtree\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfdrawtree\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-fontfile\fR \fIstring\fR
+.RS 4
+Default value: font1
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Output section"
+.PP
+\fB\-plotfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-plotter\fR \fIlist\fR
+.RS 4
+Default value: l
+.RE
+.PP
+\fB\-previewer\fR \fIlist\fR
+.RS 4
+Default value: x
+.RE
+.PP
+\fB\-iterate\fR \fIlist\fR
+.RS 4
+Default value: e
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-labeldirection\fR \fIlist\fR
+.RS 4
+Default value: m
+.RE
+.PP
+\fB\-treeangle\fR \fIfloat\fR
+.RS 4
+Default value: 90\&.0
+.RE
+.PP
+\fB\-arc\fR \fIfloat\fR
+.RS 4
+Default value: 360
+.RE
+.PP
+\fB\-labelrotation\fR \fIfloat\fR
+.RS 4
+Default value: 90\&.0
+.RE
+.PP
+\fB\-rescaled\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-bscale\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-treedepth\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.53
+.RE
+.PP
+\fB\-xmargin\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.65
+.RE
+.PP
+\fB\-ymargin\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.16
+.RE
+.PP
+\fB\-xrayshade\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.65
+.RE
+.PP
+\fB\-yrayshade\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.16
+.RE
+.PP
+\fB\-paperx\fR \fIfloat\fR
+.RS 4
+Default value: 20\&.63750
+.RE
+.PP
+\fB\-papery\fR \fIfloat\fR
+.RS 4
+Default value: 26\&.98750
+.RE
+.PP
+\fB\-pagesheight\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-pageswidth\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hpmargin\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.41275
+.RE
+.PP
+\fB\-vpmargin\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.53975
+.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
+fdrawtree 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/ffactor.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/ffactor.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/ffactor.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,85 @@
+'\" t
+.\" Title: FFACTOR
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FFACTOR" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+ffactor \- Multistate to binary recoding program
+.SH "SYNOPSIS"
+.HP \w'\fBffactor\fR\ 'u
+\fBffactor\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-anc\ \fR\fB\fIboolean\fR\fR] [\fB\-factors\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactorfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBffactor\fR\ 'u
+\fBffactor\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBffactor\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-anc\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-factors\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outfactorfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outancfile\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
+ffactor 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/ffitch.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/ffitch.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/ffitch.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,139 @@
+'\" t
+.\" Title: FFITCH
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FFITCH" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+ffitch \- Fitch\-Margoliash and Least\-Squares Distance Methods
+.SH "SYNOPSIS"
+.HP \w'\fBffitch\fR\ 'u
+\fBffitch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-power\ \fR\fB\fIfloat\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-negallowed\ \fR\fB\fIboolean\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBffitch\fR\ 'u
+\fBffitch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBffitch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-datafile\fR \fIdistances\fR
+.RS 4
+File containing one or more distance matrices
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-matrixtype\fR \fIlist\fR
+.RS 4
+Default value: s
+.RE
+.PP
+\fB\-minev\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-power\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-negallowed\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-replicates\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+ffitch 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/ffreqboot.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/ffreqboot.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/ffreqboot.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,117 @@
+'\" t
+.\" Title: FFREQBOOT
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FFREQBOOT" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+ffreqboot \- Bootstrapped genetic frequencies algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBffreqboot\fR\ 'u
+\fBffreqboot\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBffreqboot\fR\ 'u
+\fBffreqboot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBffreqboot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIfrequencies\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.SS "Additional section"
+.PP
+\fB\-test\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-regular\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fracsample\fR \fIfloat\fR
+.RS 4
+Default value: 100\&.0
+.RE
+.PP
+\fB\-blocksize\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-reps\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-justweights\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+ffreqboot 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fgendist.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fgendist.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fgendist.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: FGENDIST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FGENDIST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fgendist \- Compute genetic distances from gene frequencies
+.SH "SYNOPSIS"
+.HP \w'\fBfgendist\fR\ 'u
+\fBfgendist\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfgendist\fR\ 'u
+\fBfgendist\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfgendist\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIfrequencies\fR
+.RS 4
+File containing one or more sets of data
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: n
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-lower\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fgendist 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fkitsch.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fkitsch.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fkitsch.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,125 @@
+'\" t
+.\" Title: FKITSCH
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FKITSCH" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fkitsch \- Fitch\-Margoliash method with contemporary tips
+.SH "SYNOPSIS"
+.HP \w'\fBfkitsch\fR\ 'u
+\fBfkitsch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-power\ \fR\fB\fIfloat\fR\fR] [\fB\-negallowed\ \fR\fB\fIboolean\fR\fR] [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfkitsch\fR\ 'u
+\fBfkitsch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfkitsch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-datafile\fR \fIdistances\fR
+.RS 4
+File containing one or more distance matrices
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-matrixtype\fR \fIlist\fR
+.RS 4
+Default value: s
+.RE
+.PP
+\fB\-minev\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-power\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-negallowed\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-replicates\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fkitsch 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fmix.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fmix.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fmix.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,136 @@
+'\" t
+.\" Title: FMIX
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FMIX" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fmix \- Mixed parsimony algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfmix\fR\ 'u
+\fBfmix\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfmix\fR\ 'u
+\fBfmix\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfmix\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more data sets
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-mixfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: Wagner
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: $(infile\&.discretesize)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fmix 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fmove.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fmove.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fmove.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,109 @@
+'\" t
+.\" Title: FMOVE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FMOVE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fmove \- Interactive mixed method parsimony
+.SH "SYNOPSIS"
+.HP \w'\fBfmove\fR\ 'u
+\fBfmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBfmove\fR\ 'u
+\fBfmove\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfmove\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing data set
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-factorfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: Wagner
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: $(infile\&.discretesize)
+.RE
+.PP
+\fB\-initialtree\fR \fIlist\fR
+.RS 4
+Default value: Arbitary
+.RE
+.PP
+\fB\-screenwidth\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-screenlines\fR \fIinteger\fR
+.RS 4
+Default value: 24
+.RE
+.SS "Output section"
+.PP
+\fB\-outtreefile\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
+fmove 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fneighbor.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fneighbor.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fneighbor.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,115 @@
+'\" t
+.\" Title: FNEIGHBOR
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FNEIGHBOR" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fneighbor \- Phylogenies from distance matrix by N\-J or UPGMA method
+.SH "SYNOPSIS"
+.HP \w'\fBfneighbor\fR\ 'u
+\fBfneighbor\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-treetype\ \fR\fB\fIlist\fR\fR] \fB\-outgrno\ \fR\fB\fIinteger\fR\fR [\fB\-jumble\ \fR\fB\fItoggle\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfneighbor\fR\ 'u
+\fBfneighbor\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfneighbor\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-datafile\fR \fIdistances\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-matrixtype\fR \fIlist\fR
+.RS 4
+Default value: s
+.RE
+.PP
+\fB\-treetype\fR \fIlist\fR
+.RS 4
+Default value: n
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-jumble\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-replicates\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fneighbor 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fpars.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fpars.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fpars.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,153 @@
+'\" t
+.\" Title: FPARS
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPARS" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fpars \- Discrete character parsimony
+.SH "SYNOPSIS"
+.HP \w'\fBfpars\fR\ 'u
+\fBfpars\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBfpars\fR\ 'u
+\fBfpars\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfpars\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more data sets
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: Wagner
+.RE
+.PP
+\fB\-maxtrees\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-thorough\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-rearrange\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fpars 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fpenny.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fpenny.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fpenny.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,137 @@
+'\" t
+.\" Title: FPENNY
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPENNY" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fpenny \- Penny algorithm, branch\-and\-bound
+.SH "SYNOPSIS"
+.HP \w'\fBfpenny\fR\ 'u
+\fBfpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfpenny\fR\ 'u
+\fBfpenny\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfpenny\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more data sets
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-mixfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: Wagner
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-howmany\fR \fIinteger\fR
+.RS 4
+Default value: 1000
+.RE
+.PP
+\fB\-howoften\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-simple\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: $(infile\&.discretesize)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fpenny 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fproml.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fproml.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fproml.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,202 @@
+'\" t
+.\" Title: FPROML
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPROML" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fproml \- Protein phylogeny by maximum likelihood
+.SH "SYNOPSIS"
+.HP \w'\fBfproml\fR\ 'u
+\fBfproml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfproml\fR\ 'u
+\fBfproml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfproml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.SS "Additional section"
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-model\fR \fIlist\fR
+.RS 4
+Default value: Jones\-Taylor\-Thornton
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: Constant rate
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ngammacat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarcoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ninvarcat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-nhmmcategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hmmrates\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-hmmprobabilities\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-adjsite\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-lambda\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-rough\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-hypstate\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fproml 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fpromlk.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fpromlk.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fpromlk.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,196 @@
+'\" t
+.\" Title: FPROMLK
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPROMLK" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fpromlk \- Protein phylogeny by maximum likelihood
+.SH "SYNOPSIS"
+.HP \w'\fBfpromlk\fR\ 'u
+\fBfpromlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfpromlk\fR\ 'u
+\fBfpromlk\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfpromlk\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-model\fR \fIlist\fR
+.RS 4
+Default value: Jones\-Taylor\-Thornton
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: n
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ngammacat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarcoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ninvarcat\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarfrac\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-nhmmcategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-hmmrates\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-hmmprobabilities\fR \fIarray\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-adjsite\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-lambda\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-hypstate\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+fpromlk 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fprotdist.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fprotdist.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fprotdist.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,135 @@
+'\" t
+.\" Title: FPROTDIST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPROTDIST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fprotdist \- Protein distance algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfprotdist\fR\ 'u
+\fBfprotdist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-aacateg\ \fR\fB\fIlist\fR\fR \fB\-whichcode\ \fR\fB\fIlist\fR\fR \fB\-ease\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfprotdist\fR\ 'u
+\fBfprotdist\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfprotdist\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-ncategories\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-rate\fR \fIarray\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-method\fR \fIlist\fR
+.RS 4
+Default value: j
+.RE
+.PP
+\fB\-gamma\fR \fIlist\fR
+.RS 4
+Default value: c
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-invarcoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-aacateg\fR \fIlist\fR
+.RS 4
+Default value: G
+.RE
+.PP
+\fB\-whichcode\fR \fIlist\fR
+.RS 4
+Default value: u
+.RE
+.PP
+\fB\-ease\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.457
+.RE
+.PP
+\fB\-ttratio\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-basefreq\fR \fIarray\fR
+.RS 4
+Default value: 0\&.25 0\&.25 0\&.25 0\&.25
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fprotdist 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fprotpars.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fprotpars.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fprotpars.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,138 @@
+'\" t
+.\" Title: FPROTPARS
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FPROTPARS" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fprotpars \- Protein parsimony algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfprotpars\fR\ 'u
+\fBfprotpars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-whichcode\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBfprotpars\fR\ 'u
+\fBfprotpars\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfprotpars\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+File containing one or more sequence alignments
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-thresh\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-whichcode\fR \fIlist\fR
+.RS 4
+Default value: Universal
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-stepbox\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-ancseq\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fprotpars 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/frestboot.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/frestboot.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/frestboot.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,128 @@
+'\" t
+.\" Title: FRESTBOOT
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FRESTBOOT" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+frestboot \- Bootstrapped restriction sites algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfrestboot\fR\ 'u
+\fBfrestboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR [\fB\-enzymes\ \fR\fB\fIboolean\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfrestboot\fR\ 'u
+\fBfrestboot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfrestboot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more sets of restriction data
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.SS "Additional section"
+.PP
+\fB\-test\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-regular\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fracsample\fR \fIfloat\fR
+.RS 4
+Default value: 100\&.0
+.RE
+.PP
+\fB\-rewriteformat\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-blocksize\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-reps\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-justweights\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-enzymes\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+frestboot 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/frestdist.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/frestdist.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/frestdist.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,108 @@
+'\" t
+.\" Title: FRESTDIST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FRESTDIST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+frestdist \- Distance matrix from restriction sites or fragments
+.SH "SYNOPSIS"
+.HP \w'\fBfrestdist\fR\ 'u
+\fBfrestdist\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-restsites\ \fR\fB\fIboolean\fR\fR] [\fB\-neili\ \fR\fB\fIboolean\fR\fR] \fB\-gamma\ \fR\fB\fIboolean\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfrestdist\fR\ 'u
+\fBfrestdist\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfrestdist\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-data\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more sets of restriction data
+.RE
+.SS "Additional section"
+.PP
+\fB\-restsites\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-neili\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-gamma\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-gammacoefficient\fR \fIfloat\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-ttratio\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.0
+.RE
+.PP
+\fB\-sitelength\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.PP
+\fB\-lower\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+frestdist 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/frestml.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/frestml.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/frestml.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,134 @@
+'\" t
+.\" Title: FRESTML
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FRESTML" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+frestml \- Restriction site maximum Likelihood method
+.SH "SYNOPSIS"
+.HP \w'\fBfrestml\fR\ 'u
+\fBfrestml\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-njumble\ \fR\fB\fIinteger\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-allsites\ \fR\fB\fIboolean\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-rough\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfrestml\fR\ 'u
+\fBfrestml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfrestml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-data\fR \fIdiscretestates\fR
+.RS 4
+File containing one or more sets of restriction data
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-njumble\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-allsites\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-lengths\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sitelength\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.PP
+\fB\-global\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-rough\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-trout\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outtreefile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-treeprint\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+frestml 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fretree.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fretree.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fretree.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,91 @@
+'\" t
+.\" Title: FRETREE
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FRETREE" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fretree \- Interactive tree rearrangement
+.SH "SYNOPSIS"
+.HP \w'\fBfretree\fR\ 'u
+\fBfretree\fR \fB\-spp\ \fR\fB\fIinteger\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-format\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-vscreenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBfretree\fR\ 'u
+\fBfretree\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfretree\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-spp\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-initialtree\fR \fIlist\fR
+.RS 4
+Default value: Arbitary
+.RE
+.PP
+\fB\-format\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-screenwidth\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-vscreenwidth\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-screenlines\fR \fIinteger\fR
+.RS 4
+Default value: 24
+.RE
+.SS "Output section"
+.PP
+\fB\-outtreefile\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
+fretree 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fseqboot.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fseqboot.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fseqboot.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,131 @@
+'\" t
+.\" Title: FSEQBOOT
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FSEQBOOT" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fseqboot \- Bootstrapped sequences algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfseqboot\fR\ 'u
+\fBfseqboot\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfseqboot\fR\ 'u
+\fBfseqboot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfseqboot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.SS "Additional section"
+.PP
+\fB\-test\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-regular\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fracsample\fR \fIfloat\fR
+.RS 4
+Default value: 100\&.0
+.RE
+.PP
+\fB\-rewriteformat\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-seqtype\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-blocksize\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-reps\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-justweights\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fseqboot 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/fseqbootall.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/fseqbootall.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/fseqbootall.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,163 @@
+'\" t
+.\" Title: FSEQBOOTALL
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FSEQBOOTALL" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+fseqbootall \- Bootstrapped sequences algorithm
+.SH "SYNOPSIS"
+.HP \w'\fBfseqbootall\fR\ 'u
+\fBfseqbootall\fR \fB\-infilesequences\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-datatype\ \fR\fB\fIlist\fR\fR \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-enzymes\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBfseqbootall\fR\ 'u
+\fBfseqbootall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfseqbootall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infilesequences\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-categories\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-mixfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-ancfile\fR \fIproperties\fR
+.RS 4
+.RE
+.PP
+\fB\-weights\fR \fIproperties\fR
+.RS 4
+Weights file
+.RE
+.PP
+\fB\-factorfile\fR \fIproperties\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-datatype\fR \fIlist\fR
+.RS 4
+Default value: s
+.RE
+.PP
+\fB\-test\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-regular\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fracsample\fR \fIfloat\fR
+.RS 4
+Default value: 100\&.0
+.RE
+.PP
+\fB\-rewriteformat\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-seqtype\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-morphseqtype\fR \fIlist\fR
+.RS 4
+Default value: p
+.RE
+.PP
+\fB\-blocksize\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-reps\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-justweights\fR \fIlist\fR
+.RS 4
+Default value: d
+.RE
+.PP
+\fB\-enzymes\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-all\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-printdata\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dotdiff\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+fseqbootall 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedist.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedist.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedist.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,91 @@
+'\" t
+.\" Title: FTREEDIST
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FTREEDIST" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+ftreedist \- Distances between trees
+.SH "SYNOPSIS"
+.HP \w'\fBftreedist\fR\ 'u
+\fBftreedist\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBftreedist\fR\ 'u
+\fBftreedist\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBftreedist\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-dtype\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-pairing\fR \fIlist\fR
+.RS 4
+Default value: a
+.RE
+.PP
+\fB\-style\fR \fIlist\fR
+.RS 4
+Default value: v
+.RE
+.PP
+\fB\-noroot\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.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
+ftreedist 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
Added: trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedistpair.1e
===================================================================
--- trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedistpair.1e (rev 0)
+++ trunk/packages/embassy-phylip/trunk/debian/manpages/ftreedistpair.1e 2009-08-04 13:17:35 UTC (rev 3732)
@@ -0,0 +1,95 @@
+'\" t
+.\" Title: FTREEDISTPAIR
+.\" 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: 08/04/2009
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 3.68
+.\" Language: English
+.\"
+.TH "FTREEDISTPAIR" "1e" "08/04/2009" "EMBOSS 3.68" "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"
+ftreedistpair \- Distances between two sets of trees
+.SH "SYNOPSIS"
+.HP \w'\fBftreedistpair\fR\ 'u
+\fBftreedistpair\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-bintreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBftreedistpair\fR\ 'u
+\fBftreedistpair\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBftreedistpair\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-intreefile\fR \fItree\fR
+.RS 4
+.RE
+.PP
+\fB\-bintreefile\fR \fItree\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-dtype\fR \fIlist\fR
+.RS 4
+Default value: b
+.RE
+.PP
+\fB\-pairing\fR \fIlist\fR
+.RS 4
+Default value: l
+.RE
+.PP
+\fB\-style\fR \fIlist\fR
+.RS 4
+Default value: v
+.RE
+.PP
+\fB\-noroot\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outgrno\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-progress\fR \fIboolean\fR
+.RS 4
+Default value: N
+.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
+ftreedistpair 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
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