debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+PROGS="pxaa2cdn \
+        pxbdfit \
+        pxbdsim \
+        pxboot \
+        pxbp \
+        pxcat \
+        pxclsq \
+        pxconsq \
+        pxcontrates \
+        pxfqfilt \
+        pxlog \
+        pxlssq \
+        pxlstr \
+        pxmrca \
+        pxmrcacut \
+        pxmrcaname \
+        pxnj \
+        pxnw \
+        pxrecode \
+        pxrevcomp \
+        pxrls \
+        pxrlt \
+        pxrms \
+        pxrmt \
+        pxrr \
+        pxs2fa \
+        pxs2nex \
+        pxs2phy \
+        pxseqgen \
+        pxstrec \
+        pxsw \
+        pxt2new \
+        pxtlate \
+        pxtscale \
+        pxupgma \
+        pxvcf2fa"
+
+for progname in $PROGS ; do
+   title=`$progname --help | head -n1`
+   help2man --no-info --no-discard-stderr --help-option=" --help" \
+         --name="$title" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+   echo $AUTHOR >> $MANDIR/${progname}.1
+done
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+

debian/doc-base

+Document: phyx
+Title: Phyx: Phylogenetic tools for Unix
+Author: Joseph W. Brown and Joseph F. Walker and Stephen A. Smith
+Abstract: UNIX-style phylogenetic analyses on trees and sequences
+ phyx provides a convenient, lightweight and inclusive toolkit consisting of
+ programs spanning the wide breadth of programs utilized by researchers
+ performing phylogenomic analyses. Modeled after Unix/GNU/Linux command
+ line tools, individual programs perform a single task and operate on
+ standard I/O streams. A result of this stream-centric approach is that, for
+ most programs, only a single sequence or tree is in memory at any moment.
+ Thus, large datasets can be processed with minimal memory requirements.
+ phyx’s ever-growing complement of programs consists of over 35 programs
+ focused on exploring, manipulating, analyzing and simulating phylogenetic
+ objects (alignments, trees and MCMC logs). As with standard Unix command
+ line tools, these programs can be piped (together with non-phyx tools),
+ allowing the easy construction of efficient analytical pipelines.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/phyx/Phyxed_Manual.pdf

debian/docs

+doc/Phyxed_Manual.pdf

debian/manpages

+debian/mans/*.1