phyx (1.3+ds-2) unstable; urgency=medium

[ Olek Wojnar ] * Remove unneeded dependency on libatlas-cpp [ Andreas Tille ] * Standards-Version: 4.6.1 (routine-update) * No tab in license text (routine-update) [dgit import unpatched phyx 1.3+ds-2]
author: Andreas Tille <tille@debian.org> 2022-11-15 07:43:33 +0100
committer: Andreas Tille <tille@debian.org> 2022-11-15 07:43:33 +0100
commit: 24483f9dd4d792e540196d9e93a9967f9445b3e3 (patch)
tree: 184bae4b55de285ce355c7195fa6e8ef6d91d85e
parent: bfbc432891d9a002d9774fe6395c317c7a66ba12 (diff)
parent: 8b1e601d225d58d41bcca98ff78648a52bd55cd0 (diff)
57 files changed, 2105 insertions, 0 deletions
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..90657cf
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e0f05cd
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,105 @@
+phyx (1.3+ds-2) unstable; urgency=medium
+
+  [ Olek Wojnar ]
+  * Remove unneeded dependency on libatlas-cpp
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.6.1 (routine-update)
+  * No tab in license text (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Tue, 15 Nov 2022 07:43:33 +0100
+
+phyx (1.3+ds-1) unstable; urgency=medium
+
+  [ Nilesh Patra ]
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.1 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Refresh and remove merged patches
+  * Enhance d/u/metadata
+  * d/p/hardening.patch: Propagate hardening options
+  * d/tests/run-unit-test: Fix file locations
+  * d/p/build-more-programs.patch: Also build and vendor pxupgma pxnj
+  * d/tests/run-unit-test: Fix autopkgtests
+  * Drop link_lnopt.patch
+
+  [ Étienne Mollier ]
+  * Add i386.patch: removing -ffast-math fixes NaN errors on i387 FPU.
+
+ -- Étienne Mollier <emollier@debian.org>  Thu, 14 Apr 2022 14:53:02 +0200
+
+phyx (1.01+ds-2) unstable; urgency=medium
+
+  * Team upload
+
+  [ Nilesh Patra ]
+  * Add patch to build with g++-10
+    Closes: #957683
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.0 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * debian/copyright: use spaces rather than tabs to start continuation
+    lines.
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Nilesh Patra <npatra974@gmail.com>  Fri, 17 Apr 2020 21:56:19 +0200
+
+phyx (1.01+ds-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Removed obsolete 2to3 patch
+  * Adjusted cleanup after build
+  * Not having upstream's auto-generated src/configure in source tree
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 12 Dec 2019 12:50:28 +0100
+
+phyx (1.0+ds-1) unstable; urgency=medium
+
+  * Team upload
+
+  [ Andreas Tille ]
+  * Install Phyx_Gui
+  * Provide README.test to explain how to run test suite as user example
+
+  [ Shayan Doust ]
+  * New upstream release
+
+ -- Shayan Doust <hello@shayandoust.me>  Fri, 13 Sep 2019 02:47:52 +0100
+
+phyx (0.999+ds-2) unstable; urgency=medium
+
+  * Team upload
+
+  [ Steffen Möller ]
+  * Add new d/u/metadata file
+
+  [ Afif Elghraoui ]
+  * Remove myself from Uploaders
+
+  [ Shayan Doust ]
+  * Port couple of python files from python2 to python3
+    Closes: #937285
+  * Set debhelper 12 from 11
+
+  [ Andreas Tille ]
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Add autopkgtest
+
+ -- Shayan Doust <hello@shayandoust.me>  Wed, 11 Sep 2019 21:17:58 +0200
+
+phyx (0.999+ds-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille@debian.org>  Mon, 15 Oct 2018 16:19:59 +0200
+
+phyx (0.99+ds-1) unstable; urgency=medium
+
+  * Initial release (Closes: #855597)
+
+ -- Andreas Tille <tille@debian.org>  Sat, 08 Sep 2018 22:16:39 +0200
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..619509d
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,35 @@
+Source: phyx
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+               python3,
+               liblapack-dev,
+               libnlopt-cxx-dev,
+               libnlopt-dev,
+               libarmadillo-dev
+Standards-Version: 4.6.1
+Vcs-Browser: https://salsa.debian.org/med-team/phyx
+Vcs-Git: https://salsa.debian.org/med-team/phyx.git
+Homepage: https://github.com/FePhyFoFum/phyx
+Rules-Requires-Root: no
+
+Package: phyx
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         python3
+Description: 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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..427fede
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: phyx
+Source: https://github.com/FePhyFoFum/phyx/releases
+Files-Excluded:
+         deps
+         src/configure
+
+Files: *
+Copyright: 2014-2017 Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith
+License: GPL-3
+
+Files: debian/*
+Copyright: 2017 Afif Elghraoui <afif@debian.org>
+License: GPL-3
+
+License: GPL-3
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License.
+ .
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..d467e19
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,61 @@
+#!/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
+
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..c480403
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+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
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..6388364
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+doc/Phyxed_Manual.pdf
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..0790e4d
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+example_files/*
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..bc9d345
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+#debian/mans/*.1
diff --git a/debian/mans/pxaa2cdn.1 b/debian/mans/pxaa2cdn.1
new file mode 100644
index 0000000..7a4ace2
--- /dev/null
+++ b/debian/mans/pxaa2cdn.1
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXAA2CDN "1" "May 2018" "pxaa2cdn 0.99+ds" "User Commands"
+.SH NAME
+pxaa2cdn \- Takes in AA alignment and unaligned Nucleotide file to give a Codon Alignment.
+.SH SYNOPSIS
+.B pxaa2cdn
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Takes in AA alignment and unaligned Nucleotide file to give a Codon Alignment.
+This will get rid of any sequences found in either only the Nucleotide or the Amino Acid Alignment
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-a\fR, \fB\-\-aaseqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-n\fR, \fB\-\-nucseqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output fasta file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxbdfit.1 b/debian/mans/pxbdfit.1
new file mode 100644
index 0000000..9ea759a
--- /dev/null
+++ b/debian/mans/pxbdfit.1
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXBDFIT "1" "May 2018" "pxbdfit 0.99+ds" "User Commands"
+.SH NAME
+pxbdfit \- Birth-death inference
+.SH SYNOPSIS
+.B pxbdfit
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Birth\-death inference
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input treefile, stdin otherwise
+.TP
+\fB\-m\fR, \fB\-\-model\fR=\fI\,STRING\/\fR
+diversification model; either 'yule' or 'bd' (default)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxbdsim.1 b/debian/mans/pxbdsim.1
new file mode 100644
index 0000000..f3fc0b5
--- /dev/null
+++ b/debian/mans/pxbdsim.1
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXBDSIM "1" "May 2018" "pxbdsim 0.99+ds" "User Commands"
+.SH NAME
+pxbdsim \- Birth-death simulator.
+.SH SYNOPSIS
+.B pxbdsim
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Birth\-death simulator.
+.TP
+\fB\-e\fR, \fB\-\-extant\fR=\fI\,INT\/\fR
+number of extant species, alt to time
+.TP
+\fB\-t\fR, \fB\-\-time\fR=\fI\,INT\/\fR
+depth of the tree, alt to extant
+.TP
+\fB\-b\fR, \fB\-\-birth\fR=\fI\,DOUBLE\/\fR
+birth rate, default=1
+.TP
+\fB\-d\fR, \fB\-\-death\fR=\fI\,DOUBLE\/\fR
+death rate, default=0
+.TP
+\fB\-n\fR, \fB\-\-nreps\fR=\fI\,INT\/\fR
+number of replicates, default=1
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-s\fR, \fB\-\-showd\fR
+show dead taxa
+.TP
+\fB\-x\fR, \fB\-\-seed\fR=\fI\,INT\/\fR
+random number seed, clock otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxboot.1 b/debian/mans/pxboot.1
new file mode 100644
index 0000000..cfa8c4c
--- /dev/null
+++ b/debian/mans/pxboot.1
@@ -0,0 +1,37 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXBOOT "1" "May 2018" "pxboot 0.99+ds" "User Commands"
+.SH NAME
+pxboot \- Sequence alignment bootstrap or jackknife resampling.
+.SH SYNOPSIS
+.B pxboot
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Sequence alignment bootstrap or jackknife resampling.
+This will take fasta, fastq, phylip, and nexus inputs.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-p\fR, \fB\-\-partf\fR=\fI\,FILE\/\fR
+file listing empirical partitions: NAME = START\-STOP[\eINTERVAL]
+.TP
+\fB\-f\fR, \fB\-\-frac\fR=\fI\,DOUBLE\/\fR
+jackknife percentage, default bootstrap (i.e. \fB\-f\fR 1.0)
+.TP
+\fB\-x\fR, \fB\-\-seed\fR=\fI\,INT\/\fR
+random number seed, clock otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxbp.1 b/debian/mans/pxbp.1
new file mode 100644
index 0000000..1b71077
--- /dev/null
+++ b/debian/mans/pxbp.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXBP "1" "May 2018" "pxbp 0.99+ds" "User Commands"
+.SH NAME
+pxbp \- This will print out bipartitions found in treefile.
+.SH SYNOPSIS
+.B pxbp
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+This will print out bipartitions found in treefile.
+Can read from stdin or file.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input treefile, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxcat.1 b/debian/mans/pxcat.1
new file mode 100644
index 0000000..6a4e6d1
--- /dev/null
+++ b/debian/mans/pxcat.1
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXCAT "1" "May 2018" "pxcat 0.99+ds" "User Commands"
+.SH NAME
+pxcat \- Sequence file concatenation.
+.SH SYNOPSIS
+.B pxcat
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Sequence file concatenation.
+Can use wildcards e.g.:
+.IP
+pxcat \fB\-s\fR *.phy \fB\-o\fR my_cat_file.fa
+.SS "However, if the argument list is too long (shell limit), put filenames in a file:"
+.IP
+for x in *.phy; do echo $x >> flist.txt; done
+.SS "and call using the -f option:"
+.IP
+pxcat \fB\-f\fR flist.txt \fB\-o\fR my_cat_file.fa
+.PP
+This will take fasta, fastq, phylip, and nexus inputs.
+Individual files can be of different formats.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+list of input sequence files (space delimited)
+.TP
+\fB\-f\fR, \fB\-\-flistFILE\fR
+file listing input files (one per line)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-p\fR, \fB\-\-partf\fR=\fI\,FILE\/\fR
+output partition file, none otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxclsq.1 b/debian/mans/pxclsq.1
new file mode 100644
index 0000000..6c95ffc
--- /dev/null
+++ b/debian/mans/pxclsq.1
@@ -0,0 +1,37 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXCLSQ "1" "May 2018" "pxclsq 0.99+ds" "User Commands"
+.SH NAME
+pxclsq \- Cleans alignments by removing positions with too much ambiguous data.
+.SH SYNOPSIS
+.B pxclsq
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Cleans alignments by removing positions with too much ambiguous data.
+This will take fasta, fastq, phylip, and nexus inputs.
+Results are written in fasta format.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output fasta file, stout otherwise
+.TP
+\fB\-p\fR, \fB\-\-prop\fR=\fI\,DOUBLE\/\fR
+proportion required to be present, default=0.5
+.TP
+\fB\-a\fR, \fB\-\-aminoacid\fR
+force interpret as protein (if inference fails)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+more verbose output (i.e. if entire seqs are removed)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxconsq.1 b/debian/mans/pxconsq.1
new file mode 100644
index 0000000..3a0c853
--- /dev/null
+++ b/debian/mans/pxconsq.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXCONSQ "1" "May 2018" "pxconsq 0.99+ds" "User Commands"
+.SH NAME
+pxconsq \- Consensus sequences from nexus, phylip, or fastq to fasta.
+.SH SYNOPSIS
+.B pxconsq
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Consensus sequences from nexus, phylip, or fastq to fasta.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxcontrates.1 b/debian/mans/pxcontrates.1
new file mode 100644
index 0000000..7bc794d
--- /dev/null
+++ b/debian/mans/pxcontrates.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXCONTRATES "1" "May 2018" "pxcontrates 0.99+ds" "User Commands"
+.SH NAME
+pxcontrates \- Continuous character rate estimation with Brownian and OU.
+.SH SYNOPSIS
+.B pxcontrates
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Continuous character rate estimation with Brownian and OU.
+This will take fasta, phylip (and soon nexus) inputs.
+Can read from stdin or file.
+.TP
+\fB\-c\fR, \fB\-\-charf\fR=\fI\,FILE\/\fR
+input character file, stdin otherwise
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-a\fR, \fB\-\-analysis\fR=\fI\,NUM\/\fR
+analysis type (0=anc[DEFAULT], 1=ratetest)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxfqfilt.1 b/debian/mans/pxfqfilt.1
new file mode 100644
index 0000000..e34fa42
--- /dev/null
+++ b/debian/mans/pxfqfilt.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXFQFILT "1" "May 2018" "pxfqfilt 0.99+ds" "User Commands"
+.SH NAME
+pxfqfilt \- Filter fastq files by mean quality.
+.SH SYNOPSIS
+.B pxfqfilt
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Filter fastq files by mean quality.
+Can read from stdin or file.
+.TP
+\fB\-m\fR, \fB\-\-mean\fR=\fI\,VALUE\/\fR
+mean value under which seqs are filtered
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxlog.1 b/debian/mans/pxlog.1
new file mode 100644
index 0000000..d3fb950
--- /dev/null
+++ b/debian/mans/pxlog.1
@@ -0,0 +1,52 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXLOG "1" "May 2018" "pxlog 0.99+ds" "User Commands"
+.SH NAME
+pxlog \- MCMC log file manipulator.
+.SH SYNOPSIS
+.B pxlog
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+MCMC log file manipulator.
+Can combine and resample parameters or trees across files.
+Log files need not contain the same number of samples.
+Input files may be indicated using wildcards e.g. '*.trees'
+Parameter log files are expected to be whitespace delimited.
+*NOTE* All values are in terms of number of SAMPLES (NOT generations).
+.TP
+\fB\-p\fR, \fB\-\-parmf\fR=\fI\,FILE\/\fR
+input parameter log file(s)
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree log file(s)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-b\fR, \fB\-\-burnin\fR=\fI\,INT\/\fR
+number of samples to exclude at the beginning of a file
+.TP
+\fB\-n\fR, \fB\-\-thin\fR=\fI\,INT\/\fR
+interval of resampling
+.TP
+\fB\-r\fR, \fB\-\-rand\fR=\fI\,INT\/\fR
+number of random samples (without replacement) not yet implemented!
+.TP
+\fB\-i\fR, \fB\-\-info\fR
+calculate log file attributes and exit
+.TP
+\fB\-x\fR, \fB\-\-seed\fR=\fI\,INT\/\fR
+random number seed, clock otherwise
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+make the output more verbose
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxlssq.1 b/debian/mans/pxlssq.1
new file mode 100644
index 0000000..6fa30b5
--- /dev/null
+++ b/debian/mans/pxlssq.1
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXLSSQ "1" "May 2018" "pxlssq 0.99+ds" "User Commands"
+.SH NAME
+pxlssq \- Print sequence file summary
+.SH SYNOPSIS
+.B pxlssq
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Print sequence file summary
+By default returns all properties. Alternatively choose 1 property.
+This will take fasta, phylip or nexus file formats
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input seq file, stdin otherwise
+.TP
+\fB\-i\fR, \fB\-\-indiv\fR
+output stats for individual sequences
+.TP
+\fB\-n\fR, \fB\-\-nseq\fR
+return the number of sequences
+.TP
+\fB\-c\fR, \fB\-\-nchar\fR
+return the number of characters (only if aligned)
+\- for unaligned seqs, use with \fB\-i\fR flag
+.TP
+\fB\-l\fR, \fB\-\-labels\fR
+return all taxon labels (one per line)
+.TP
+\fB\-p\fR, \fB\-\-prot\fR
+force interpret as protein (if inference fails)
+.TP
+\fB\-a\fR, \fB\-\-aligned\fR
+return whether sequences are aligned (same length)
+.TP
+\fB\-f\fR, \fB\-\-freqs\fR
+return character state frequencies
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output stats file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxlstr.1 b/debian/mans/pxlstr.1
new file mode 100644
index 0000000..37435dd
--- /dev/null
+++ b/debian/mans/pxlstr.1
@@ -0,0 +1,52 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXLSTR "1" "May 2018" "pxlstr 0.99+ds" "User Commands"
+.SH NAME
+pxlstr \- Print tree summary
+.SH SYNOPSIS
+.B pxlstr
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Print tree summary
+By default returns all properties. Alternatively choose 1 property.
+This will take newick or nexus files
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-r\fR, \fB\-\-rooted\fR
+return whether the tree is rooted
+.TP
+\fB\-a\fR, \fB\-\-age\fR
+return the height of root (must be rooted and ultrametric)
+.TP
+\fB\-n\fR, \fB\-\-ntips\fR
+return the number of terminals
+.TP
+\fB\-u\fR, \fB\-\-ultrametric\fR
+return whether tree is ultrametric
+.TP
+\fB\-b\fR, \fB\-\-binary\fR
+return whether tree is binary
+.TP
+\fB\-l\fR, \fB\-\-length\fR
+return the length of the tree
+.TP
+\fB\-i\fR, \fB\-\-tiplabels\fR
+return all tip labels (one per line)
+.TP
+\fB\-v\fR, \fB\-\-rtvar\fR
+return root\-to\-tip variance
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output tree file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxmrca.1 b/debian/mans/pxmrca.1
new file mode 100644
index 0000000..371ee7b
--- /dev/null
+++ b/debian/mans/pxmrca.1
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXMRCA "1" "May 2018" "pxmrca 0.99+ds" "User Commands"
+.SH NAME
+pxmrca \- Get the number of descendant tips of internal nodes specified by mrca statements.
+.SH SYNOPSIS
+.B pxmrcacut
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Get the number of descendant tips of internal nodes specified by mrca statements.
+Takes in newick tree and MRCA file with format:
+MRCANAME = tip1 tip2 ...
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input newick tree file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output newick file, stout otherwise
+.TP
+\fB\-m\fR, \fB\-\-mrca\fR=\fI\,FILE\/\fR
+file containing MRCA declarations
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxmrcacut.1 b/debian/mans/pxmrcacut.1
new file mode 100644
index 0000000..9684be9
--- /dev/null
+++ b/debian/mans/pxmrcacut.1
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXMRCACUT "1" "May 2018" "pxmrcacut 0.99+ds" "User Commands"
+.SH NAME
+pxmrcacut \- Extract subclade(s) from tree(s).
+.SH SYNOPSIS
+.B pxmrcacut
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Extract subclade(s) from tree(s).
+Takes in newick tree and MRCA file with format:
+MRCANAME = tip1 tip2 ...
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input newick tree file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output newick file, stout otherwise
+.TP
+\fB\-m\fR, \fB\-\-mrca\fR=\fI\,FILE\/\fR
+file containing MRCA declarations
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxmrcaname.1 b/debian/mans/pxmrcaname.1
new file mode 100644
index 0000000..5e85300
--- /dev/null
+++ b/debian/mans/pxmrcaname.1
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXMRCANAME "1" "May 2018" "pxmrcaname 0.99+ds" "User Commands"
+.SH NAME
+pxmrcaname \- Label internal nodes with clade names.
+.SH SYNOPSIS
+.B pxmrcaname
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Label internal nodes with clade names.
+Takes in newick tree and MRCA file with format:
+MRCANAME = tip1 tip2 ...
+If no MRCA file is present, this will label anything
+that isn't labeled
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input newick tree file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output newick file, stout otherwise
+.TP
+\fB\-m\fR, \fB\-\-mrca\fR=\fI\,FILE\/\fR
+file containing MRCA declarations
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxnj.1 b/debian/mans/pxnj.1
new file mode 100644
index 0000000..1294843
--- /dev/null
+++ b/debian/mans/pxnj.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXNJ "1" "May 2018" "pxnj 0.99+ds" "User Commands"
+.SH NAME
+pxnj \- Basic Neighbour-Joining Tree Maker.
+.SH SYNOPSIS
+.B pxnj
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Basic Neighbour\-Joining Tree Maker.
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output newick file, stout otherwise
+.TP
+\fB\-n\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
+number of threads, default=1
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxnw.1 b/debian/mans/pxnw.1
new file mode 100644
index 0000000..f150f52
--- /dev/null
+++ b/debian/mans/pxnw.1
@@ -0,0 +1,45 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXNW "1" "May 2018" "pxnw 0.99+ds" "User Commands"
+.SH NAME
+pxnw \- Conduct Needleman-Wunsch analysis for all the seqs in a file.
+.SH SYNOPSIS
+.B pxnw
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Conduct Needleman\-Wunsch analysis for all the seqs in a file.
+This will take fasta, fastq, phylip, and nexus inputs.
+Output is a list of the scores and distances (and the alignments
+if asked).
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output score/distance file, stout otherwise
+.TP
+\fB\-a\fR, \fB\-\-outalnf\fR=\fI\,FILE\/\fR
+output sequence file, won't output otherwise
+.TP
+\fB\-t\fR, \fB\-\-seqtype\fR=\fI\,INT\/\fR
+sequence type, default=DNA (DNA=0,AA=1)
+.TP
+\fB\-m\fR, \fB\-\-matrix\fR=\fI\,FILE\/\fR
+scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62
+.TP
+\fB\-n\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
+number of threads (open mp), default=2
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+make the output more verbose, turns off parallel
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrecode.1 b/debian/mans/pxrecode.1
new file mode 100644
index 0000000..4f6ab5d
--- /dev/null
+++ b/debian/mans/pxrecode.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRECODE "1" "May 2018" "pxrecode 0.99+ds" "User Commands"
+.SH NAME
+pxrecode \- Sequence recoding. Currently only to RY, but more coming.
+.SH SYNOPSIS
+.B pxrecode
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Sequence recoding. Currently only to RY, but more coming.
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrevcomp.1 b/debian/mans/pxrevcomp.1
new file mode 100644
index 0000000..967eddd
--- /dev/null
+++ b/debian/mans/pxrevcomp.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXREVCOMP "1" "May 2018" "pxrevcomp 0.99+ds" "User Commands"
+.SH NAME
+pxrevcomp \- Reverse complement sequences from nexus, phylip, or fastq to fasta.
+.SH SYNOPSIS
+.B pxrevcomp
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Reverse complement sequences from nexus, phylip, or fastq to fasta.
+Can read from stdin or file, but output is fasta.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrls.1 b/debian/mans/pxrls.1
new file mode 100644
index 0000000..41f42ab
--- /dev/null
+++ b/debian/mans/pxrls.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRLS "1" "May 2018" "pxrls 0.99+ds" "User Commands"
+.SH NAME
+pxrls \- Taxon relabelling for alignments.
+.SH SYNOPSIS
+.B pxrls
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Taxon relabelling for alignments.
+This will take fasta, phylip or nexus file formats
+Two ordered lists of taxa, \fB\-c\fR (current) and \fB\-n\fR (new) must be provided.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input seq file, stdin otherwise
+.TP
+\fB\-c\fR, \fB\-\-cnames\fR=\fI\,FILE\/\fR
+file containing current taxon labels (one per line)
+.TP
+\fB\-n\fR, \fB\-\-nnames\fR=\fI\,FILE\/\fR
+file containing new taxon labels (one per line)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrlt.1 b/debian/mans/pxrlt.1
new file mode 100644
index 0000000..133bdf6
--- /dev/null
+++ b/debian/mans/pxrlt.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRLT "1" "May 2018" "pxrlt 0.99+ds" "User Commands"
+.SH NAME
+pxrlt \- Taxon relabelling for trees.
+.SH SYNOPSIS
+.B pxrlt
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Taxon relabelling for trees.
+This will take nexus and newick inputs.
+Two ordered lists of taxa, \fB\-c\fR (current) and \fB\-n\fR (new) must be provided.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-c\fR, \fB\-\-cnames\fR=\fI\,FILE\/\fR
+file containing current taxon labels (one per line)
+.TP
+\fB\-n\fR, \fB\-\-nnames\fR=\fI\,FILE\/\fR
+file containing new taxon labels (one per line)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrms.1 b/debian/mans/pxrms.1
new file mode 100644
index 0000000..2691908
--- /dev/null
+++ b/debian/mans/pxrms.1
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRMS "1" "May 2018" "pxrms 0.99+ds" "User Commands"
+.SH NAME
+pxrms \- Removes unwanted sequences
+.SH SYNOPSIS
+.B pxrms
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Removes unwanted sequences
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input nucleotide sequence file, stdin otherwise
+.TP
+\fB\-n\fR, \fB\-\-names\fR=\fI\,CSL\/\fR
+names sep by commas (NO SPACES!)
+.TP
+\fB\-f\fR, \fB\-\-namesf\fR=\fI\,FILE\/\fR
+names in a file (each on a line)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output aa sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrmt.1 b/debian/mans/pxrmt.1
new file mode 100644
index 0000000..dd6e257
--- /dev/null
+++ b/debian/mans/pxrmt.1
@@ -0,0 +1,36 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRMT "1" "May 2018" "pxrmt 0.99+ds" "User Commands"
+.SH NAME
+pxrmt \- This will remove tips from a tree file and produce newick
+.SH SYNOPSIS
+.B pxrmt
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+This will remove tips from a tree file and produce newick
+Can read from stdin or file
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-n\fR, \fB\-\-names\fR=\fI\,CSL\/\fR
+names sep by commas (NO SPACES!)
+.TP
+\fB\-f\fR, \fB\-\-namesf\fR=\fI\,FILE\/\fR
+names in a file (each on a line)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output tree file, stout otherwise
+.TP
+\fB\-s\fR, \fB\-\-silent\fR
+suppress warnings of missing tips
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxrr.1 b/debian/mans/pxrr.1
new file mode 100644
index 0000000..58efab4
--- /dev/null
+++ b/debian/mans/pxrr.1
@@ -0,0 +1,36 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXRR "1" "May 2018" "pxrr 0.99+ds" "User Commands"
+.SH NAME
+pxrr \- This will reroot (or unroot) a tree file and produce a newick.
+.SH SYNOPSIS
+.B pxrr
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+This will reroot (or unroot) a tree file and produce a newick.
+Can read from stdin or file.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-g\fR, \fB\-\-outgroups\fR=\fI\,CSL\/\fR
+outgroup sep by commas (NO SPACES!)
+.TP
+\fB\-u\fR, \fB\-\-unroot\fR
+unroot the tree
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output tree file, stout otherwise
+.TP
+\fB\-s\fR, \fB\-\-silent\fR
+do not error if outgroup(s) not found
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxs2fa.1 b/debian/mans/pxs2fa.1
new file mode 100644
index 0000000..1153e95
--- /dev/null
+++ b/debian/mans/pxs2fa.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXS2FA "1" "May 2018" "pxs2fa 0.99+ds" "User Commands"
+.SH NAME
+pxs2fa \- Convert seqfiles from nexus,phylip, fastq to fasta.
+.SH SYNOPSIS
+.B pxs2fa
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Convert seqfiles from nexus,phylip, fastq to fasta.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-u\fR, \fB\-\-uppercase\fR
+export characters in uppercase
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxs2nex.1 b/debian/mans/pxs2nex.1
new file mode 100644
index 0000000..51805c9
--- /dev/null
+++ b/debian/mans/pxs2nex.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXS2NEX "1" "May 2018" "pxs2nex 0.99+ds" "User Commands"
+.SH NAME
+pxs2nex \- Convert seqfiles from nexus, phylip, or fastq to nexus.
+.SH SYNOPSIS
+.B pxs2nex
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Convert seqfiles from nexus, phylip, or fastq to nexus.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-u\fR, \fB\-\-uppercase\fR
+export characters in uppercase
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxs2phy.1 b/debian/mans/pxs2phy.1
new file mode 100644
index 0000000..90b61e9
--- /dev/null
+++ b/debian/mans/pxs2phy.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXS2PHY "1" "May 2018" "pxs2phy 0.99+ds" "User Commands"
+.SH NAME
+pxs2phy \- Convert seqfiles from nexus, phylip, or fastq to phylip.
+.SH SYNOPSIS
+.B pxs2phy
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Convert seqfiles from nexus, phylip, or fastq to phylip.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output sequence file, stout otherwise
+.TP
+\fB\-u\fR, \fB\-\-uppercase\fR
+export characters in uppercase
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxseqgen.1 b/debian/mans/pxseqgen.1
new file mode 100644
index 0000000..ed8ce76
--- /dev/null
+++ b/debian/mans/pxseqgen.1
@@ -0,0 +1,74 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXSEQGEN "1" "May 2018" "pxseqgen 0.99+ds" "User Commands"
+.SH NAME
+pxseqgen \- Basic sequence simulator under the GTR model.
+.SH SYNOPSIS
+.B pxseqgen
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Basic sequence simulator under the GTR model.
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input treefile, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output seq file, stout otherwise
+.TP
+\fB\-l\fR, \fB\-\-length\fR=\fI\,INT\/\fR
+length of sequences to generate. default is 1000
+.TP
+\fB\-b\fR, \fB\-\-basef\fR=\fI\,Input\/\fR
+comma\-delimited base freqs in order: A,C,G,T. default is equal
+.TP
+\fB\-g\fR, \fB\-\-gamma\fR=\fI\,INT\/\fR
+gamma shape value. default is no rate variation
+.TP
+\fB\-i\fR, \fB\-\-pinvar\fR=\fI\,FLOAT\/\fR
+proportion of invariable sites. default is 0.0
+.TP
+\fB\-r\fR, \fB\-\-ratemat\fR=\fI\,Input\/\fR
+comma\-delimited input values for rate matrix. default is JC69
+order: A<\->C,A<\->G,A<\->T,C<\->G,C<\->T,G<\->T
+.TP
+\fB\-w\fR, \fB\-\-aaratemat\fR=\fI\,Input\/\fR
+comma\-delimited amino acid rate matrix. default is all freqs equal
+order is ARNDCQEGHILKMFPSTWYV
+.HP
+\fB\-q\fR, \fB\-\-aabasefreq\fR=\fI\,Input\/\fR AA frequencies, order: ARNDCQEGHILKMFPSTWYV
+.TP
+\fB\-c\fR, \fB\-\-protein\fR
+run as amino acid
+.TP
+\fB\-n\fR, \fB\-\-nreps\fR=\fI\,INT\/\fR
+number of replicates
+.TP
+\fB\-x\fR, \fB\-\-seed\fR=\fI\,INT\/\fR
+random number seed, clock otherwise
+.TP
+\fB\-a\fR, \fB\-\-ancestors\fR
+print the ancestral node sequences. default is no
+use \fB\-p\fR for the nodes labels
+.TP
+\fB\-p\fR, \fB\-\-printnodelabels\fR
+print newick with internal node labels. default is no
+.TP
+\fB\-m\fR, \fB\-\-multimodel\fR=\fI\,Input\/\fR specify multiple models across tree
+input is as follows:
+.TP
+A<\->C,A<\->G,A<\->T,C<\->G,C<\->T,G<\->T,Node#,A<\->C,A<\->G,A<\->T,C<\->G,C<\->T,G<\->T
+EX:.3,.3,.3,.3,.3,1,.3,.3,.2,.5,.4
+.TP
+\fB\-k\fR, \fB\-\-rootseq\fR=\fI\,STRING\/\fR
+set root sequence. default is random (from basefreqs)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxstrec.1 b/debian/mans/pxstrec.1
new file mode 100644
index 0000000..0e73e84
--- /dev/null
+++ b/debian/mans/pxstrec.1
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXSTREC "1" "May 2018" "pxstrec 0.99+ds" "User Commands"
+.SH NAME
+pxstrec \- This will conduct state reconstruction analyses.
+.SH SYNOPSIS
+.B pxstrec
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+This will conduct state reconstruction analyses.
+.TP
+\fB\-d\fR, \fB\-\-dataf\fR=\fI\,FILE\/\fR
+input data file
+.TP
+\fB\-w\fR, \fB\-\-datawide\fR
+data is in wide format so (001 instead of 2)
+.TP
+\fB\-z\fR, \fB\-\-dataz\fR
+data is in probability format (0,1,0,0)
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file
+.TP
+\fB\-c\fR, \fB\-\-conf\fR=\fI\,FILE\/\fR
+configuration file
+.TP
+\fB\-o\fR, \fB\-\-outanc\fR=\fI\,FILE\/\fR
+output file for ancestral calc
+.HP
+\fB\-n\fR, \fB\-\-outstnum\fR=\fI\,FILE\/\fR output file for stochastic mapping number
+.HP
+\fB\-a\fR, \fB\-\-outstnumany\fR=\fI\,FILE\/\fR output file for stochastic mapping number any
+.HP
+\fB\-m\fR, \fB\-\-outsttim\fR=\fI\,FILE\/\fR output file for stochastic mapping duration
+.TP
+\fB\-p\fR, \fB\-\-periods\fR=\fI\,NUMS\/\fR
+comma separated times
+.TP
+\fB\-l\fR, \fB\-\-logf\fR=\fI\,FILE\/\fR
+log file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxsw.1 b/debian/mans/pxsw.1
new file mode 100644
index 0000000..44dd244
--- /dev/null
+++ b/debian/mans/pxsw.1
@@ -0,0 +1,45 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXSW "1" "May 2018" "pxsw 0.99+ds" "User Commands"
+.SH NAME
+pxsw \- Conduct Smith-Waterman analysis for all the seqs in a file.
+.SH SYNOPSIS
+.B pxsw
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Conduct Smith\-Waterman analysis for all the seqs in a file.
+This will take fasta, fastq, phylip, and nexus inputs.
+Output is a list of the scores and distances (and the alignments
+if asked).
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output score/distance file, stout otherwise
+.TP
+\fB\-a\fR, \fB\-\-outalnf\fR=\fI\,FILE\/\fR
+output sequence file, won't output otherwise
+.TP
+\fB\-t\fR, \fB\-\-seqtype\fR=\fI\,INT\/\fR
+sequence type, default=DNA (DNA=0,AA=1)
+.TP
+\fB\-m\fR, \fB\-\-matrix\fR=\fI\,FILE\/\fR
+scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62
+.TP
+\fB\-n\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
+number of threads (open mp), default=2
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+make the output more verbose, turns off parallel
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxt2new.1 b/debian/mans/pxt2new.1
new file mode 100644
index 0000000..6f0f245
--- /dev/null
+++ b/debian/mans/pxt2new.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXT2NEW "1" "May 2018" "pxt2new 0.99+ds" "User Commands"
+.SH NAME
+pxt2new \- This will convert a tree file to newick.
+.SH SYNOPSIS
+.B pxt2new
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+This will convert a tree file to newick.
+Can read from stdin or file.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output tree file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxtlate.1 b/debian/mans/pxtlate.1
new file mode 100644
index 0000000..f4c2ac4
--- /dev/null
+++ b/debian/mans/pxtlate.1
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXTLATE "1" "May 2018" "pxtlate 0.99+ds" "User Commands"
+.SH NAME
+pxtlate \- Translate DNA alignment to amino acids.
+.SH SYNOPSIS
+.B pxtlate
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Translate DNA alignment to amino acids.
+NOTE: assumes sequences are in frame.
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input nucleotide sequence file, stdin otherwise
+.TP
+\fB\-t\fR, \fB\-\-table\fR=\fI\,STRING\/\fR
+which translation table to use. currently available:
+\&'std' (standard, default)
+\&'vmt' (vertebrate mtDNA)
+\&'ivmt' (invertebrate mtDNA)
+\&'ymt' (yeast mtDNA)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output aa sequence file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxtscale.1 b/debian/mans/pxtscale.1
new file mode 100644
index 0000000..6c786ed
--- /dev/null
+++ b/debian/mans/pxtscale.1
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXTSCALE "1" "May 2018" "pxtscale 0.99+ds" "User Commands"
+.SH NAME
+pxtscale \- Tree rescaling by providing either scaling factor or root height.
+.SH SYNOPSIS
+.B pxtscale
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Tree rescaling by providing either scaling factor or root height.
+This will take nexus and newick inputs.
+.TP
+\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
+input tree file, stdin otherwise
+.TP
+\fB\-s\fR, \fB\-\-scale\fR=\fI\,DOUBLE\/\fR
+edge length scaling factor
+.HP
+\fB\-r\fR, \fB\-\-rootheight\fR=\fI\,DOUBLE\/\fR height of root (tree must be ultrametric)
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxupgma.1 b/debian/mans/pxupgma.1
new file mode 100644
index 0000000..0f16a91
--- /dev/null
+++ b/debian/mans/pxupgma.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXUPGMA "1" "May 2018" "pxupgma 0.99+ds" "User Commands"
+.SH NAME
+pxupgma \- Basic UPGMA Tree Maker.
+.SH SYNOPSIS
+.B pxupgma
+[\fI\,OPTION\/\fR]...
+.SH DESCRIPTION
+Basic UPGMA Tree Maker.
+This will take fasta, fastq, phylip, and nexus inputs.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input sequence file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output newick file, stout otherwise
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR,  \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/pxvcf2fa.1 b/debian/mans/pxvcf2fa.1
new file mode 100644
index 0000000..2a49ac8
--- /dev/null
+++ b/debian/mans/pxvcf2fa.1
@@ -0,0 +1,31 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PXVCF2FA "1" "May 2018" "pxvcf2fa 0.99+ds" "User Commands"
+.SH NAME
+pxvcf2fa \- Convert vcf file to fasta.
+.SH SYNOPSIS
+.B pxvcf2fa
+[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
+.SH DESCRIPTION
+Convert vcf file to fasta.
+Currently only handles haploid data; phased data will come soon.
+Can read from stdin or file.
+.TP
+\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
+input vcf file, stdin otherwise
+.TP
+\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
+output fasta sequence file, stout otherwise
+.TP
+\fB\-u\fR, \fB\-\-uppercase\fR
+export characters in uppercase
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+display version and exit
+.SH "REPORTING BUGS"
+Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
+phyx home page: <https://github.com/FePhyFoFum/phyx>
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/patches/build-more-programs.patch b/debian/patches/build-more-programs.patch
new file mode 100644
index 0000000..c84c07c
--- /dev/null
+++ b/debian/patches/build-more-programs.patch
@@ -0,0 +1,14 @@
+Description: Also build and vendor pxupgma pxnj
+Author: Nilesh Patra <nilesh@debian.org>
+Last-Update: 2021-07-10
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -357,7 +357,7 @@
+ %.o: ./%.cpp ./%.h
+ 	$(CXX) $(CXXFLAGS) $(OPT_FLAGS) $(CPPFLAGS) $(LDFLAGS) -c -fmessage-length=0 -MMD -MP -MF "$(@:%.o=%.d)" -o "$@" "$<"
+ 
+-PROGS := pxaa2cdn pxbdsim pxboot pxbp pxcat pxclsq pxcltr pxcolt pxcomp pxconsq pxfqfilt pxlog pxlssq pxlstr pxmono pxmrca pxmrcacut pxmrcaname pxnw pxpoly pxrecode pxrevcomp pxrls pxrlt pxrmk pxrms pxrmt pxrr pxs2fa pxs2nex pxs2phy pxseqgen pxssort pxsstat pxsw pxt2new pxt2nex pxtcol pxtcomb pxtgen pxtlate pxtrt pxtscale pxvcf2fa $(NLOPT_PROGRAMS)
++PROGS := pxaa2cdn pxbdsim pxboot pxbp pxcat pxclsq pxcltr pxcolt pxcomp pxconsq pxfqfilt pxlog pxlssq pxlstr pxmono pxmrca pxmrcacut pxmrcaname pxnw pxpoly pxrecode pxrevcomp pxrls pxupgma pxrlt pxnj pxrmk pxrms pxrmt pxrr pxs2fa pxs2nex pxs2phy pxseqgen pxssort pxsstat pxsw pxt2new pxt2nex pxtcol pxtcomb pxtgen pxtlate pxtrt pxtscale pxvcf2fa $(NLOPT_PROGRAMS)
+ 
+ # default all target
+ all: $(PROGS)
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..cd62e62
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,344 @@
+Description: Propagate hardening options in the build
+Author: Nilesh Patra <nilesh@debian.org>
+Last-Update: 2021-04-22
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -352,10 +352,10 @@
+ #./state_reconstructor_simple.d \
+ 
+ main_%.o: ./main_%.cpp
+-	$(CXX) $(OPT_FLAGS) $(CPPFLAGS) $(LDFLAGS) -c -fmessage-length=0 -MMD -MP -MF "$(@:%.o=%.d)" -o "$@" "$<"
++	$(CXX) $(CXXFLAGS) $(OPT_FLAGS) $(CPPFLAGS) $(LDFLAGS) -c -fmessage-length=0 -MMD -MP -MF "$(@:%.o=%.d)" -o "$@" "$<"
+ 
+ %.o: ./%.cpp ./%.h
+-	$(CXX) $(OPT_FLAGS) $(CPPFLAGS) $(LDFLAGS) -c -fmessage-length=0 -MMD -MP -MF "$(@:%.o=%.d)" -o "$@" "$<"
++	$(CXX) $(CXXFLAGS) $(OPT_FLAGS) $(CPPFLAGS) $(LDFLAGS) -c -fmessage-length=0 -MMD -MP -MF "$(@:%.o=%.d)" -o "$@" "$<"
+ 
+ PROGS := pxaa2cdn pxbdsim pxboot pxbp pxcat pxclsq pxcltr pxcolt pxcomp pxconsq pxfqfilt pxlog pxlssq pxlstr pxmono pxmrca pxmrcacut pxmrcaname pxnw pxpoly pxrecode pxrevcomp pxrls pxrlt pxrmk pxrms pxrmt pxrr pxs2fa pxs2nex pxs2phy pxseqgen pxssort pxsstat pxsw pxt2new pxt2nex pxtcol pxtcomb pxtgen pxtlate pxtrt pxtscale pxvcf2fa $(NLOPT_PROGRAMS)
+ 
+@@ -366,102 +366,102 @@
+ 
+ pxlssq: $(CPP_OBJS) $(SEQ_OBJS) $(LS_SQ_OBJ)
+ 	@echo 'bulding pxlssq'
+-	$(CXX) -o "pxlssq" $(OPT_FLAGS) $(LS_SQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxlssq" $(OPT_FLAGS) $(LS_SQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxconsq: $(CPP_OBJS) $(SEQ_OBJS) $(CONSEQ_OBJ)
+ 	@echo 'building pxconsq'
+-	$(CXX) -o "pxconsq" $(OPT_FLAGS) $(CONSEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxconsq" $(OPT_FLAGS) $(CONSEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxclsq: $(CPP_OBJS) $(SEQ_OBJS) $(CLSQ_OBJ)
+ 	@echo 'building pxclsq'
+-	$(CXX) -o "pxclsq" $(OPT_FLAGS) $(CLSQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxclsq" $(OPT_FLAGS) $(CLSQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrms: $(CPP_OBJS) $(SEQ_OBJS) $(RMS_OBJ)
+ 	@echo 'building pxrms'
+-	$(CXX) -o "pxrms" $(OPT_FLAGS) $(RMS_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrms" $(OPT_FLAGS) $(RMS_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxaa2cdn: $(CPP_OBJS) $(SEQ_OBJS) $(AA2C_OBJ)
+ 	@echo 'building pxaa2cdn'
+-	$(CXX) -o "pxaa2cdn" $(OPT_FLAGS) $(AA2C_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxaa2cdn" $(OPT_FLAGS) $(AA2C_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxs2fa: $(CPP_OBJS) $(SEQ_OBJS) $(2FA_OBJ)
+ 	@echo 'building pxs2fa'
+-	$(CXX) -o "pxs2fa" $(OPT_FLAGS) $(2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxs2fa" $(OPT_FLAGS) $(2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxs2phy: $(CPP_OBJS) $(SEQ_OBJS) $(2PHY_OBJ)
+ 	@echo 'building pxs2phy'
+-	$(CXX) -o "pxs2phy" $(OPT_FLAGS) $(2PHY_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxs2phy" $(OPT_FLAGS) $(2PHY_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxs2nex: $(CPP_OBJS) $(SEQ_OBJS) $(2NEX_OBJ)
+ 	@echo 'building pxs2nex'
+-	$(CXX) -o "pxs2nex" $(OPT_FLAGS) $(2NEX_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxs2nex" $(OPT_FLAGS) $(2NEX_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxfqfilt: $(CPP_OBJS) $(SEQ_OBJS) $(FQFILT_OBJ)
+ 	@echo 'building pxfqfilt'
+-	$(CXX) -o "pxfqfilt" $(OPT_FLAGS) $(FQFILT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxfqfilt" $(OPT_FLAGS) $(FQFILT_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrevcomp: $(CPP_OBJS) $(SEQ_OBJS) $(REVCOMP_OBJ)
+ 	@echo 'building pxrevcomp'
+-	$(CXX) -o "pxrevcomp" $(OPT_FLAGS) $(REVCOMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrevcomp" $(OPT_FLAGS) $(REVCOMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxnw: $(CPP_OBJS) $(SEQ_OBJS) $(NW_OBJ)
+ 	@echo 'building pxnw'
+-	$(CXX) -o "pxnw" $(OPT_FLAGS) $(NW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxnw" $(OPT_FLAGS) $(NW_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxsw: $(CPP_OBJS) $(SEQ_OBJS) $(SW_OBJ)
+ 	@echo 'building pxsw'
+-	$(CXX) -o "pxsw" $(OPT_FLAGS) $(SW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxsw" $(OPT_FLAGS) $(SW_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxboot: $(CPP_OBJS) $(SEQ_OBJS) $(SEQSAMP_OBJ)
+ 	@echo 'building pxboot'
+-	$(CXX) -o "pxboot" $(OPT_FLAGS) $(SEQSAMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxboot" $(OPT_FLAGS) $(SEQSAMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxtlate: $(CPP_OBJS) $(SEQ_OBJS) $(TLATE_OBJ)
+ 	@echo 'building pxtlate'
+-	$(CXX) -o "pxtlate" $(OPT_FLAGS) $(TLATE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtlate" $(OPT_FLAGS) $(TLATE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxcat: $(CPP_OBJS) $(SEQ_OBJS) $(CONCAT_OBJ)
+ 	@echo 'building pxcat'
+-	$(CXX) -o "pxcat" $(OPT_FLAGS) $(CONCAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxcat" $(OPT_FLAGS) $(CONCAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxsstat: $(CPP_OBJS) $(SEQ_OBJS) $(SSTAT_OBJ)
+ 	@echo 'building pxsstat'
+-	$(CXX) -o "pxsstat" $(OPT_FLAGS) $(SSTAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxsstat" $(OPT_FLAGS) $(SSTAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrecode: $(CPP_OBJS) $(SEQ_OBJS) $(SEQRECODE_OBJ)
+ 	@echo 'building pxrecode'
+-	$(CXX) -o "pxrecode" $(OPT_FLAGS) $(SEQRECODE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrecode" $(OPT_FLAGS) $(SEQRECODE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxssort: $(CPP_OBJS) $(SEQ_OBJS) $(SSORT_OBJ)
+ 	@echo 'building pxssort'
+-	$(CXX) -o "pxssort" $(OPT_FLAGS) $(SSORT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxssort" $(OPT_FLAGS) $(SSORT_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxcomp: $(CPP_OBJS) $(SEQ_OBJS) $(COMPTEST_OBJ)
+ 	@echo 'building pxcomp'
+-	$(CXX) -o "pxcomp" $(OPT_FLAGS) $(COMPTEST_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxcomp" $(OPT_FLAGS) $(COMPTEST_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxvcf2fa: $(CPP_OBJS) $(SEQ_OBJS) $(VCF2FA_OBJ)
+ 	@echo 'building pxvcf2fa'
+-	$(CXX) -o "pxvcf2fa" $(OPT_FLAGS) $(VCF2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxvcf2fa" $(OPT_FLAGS) $(VCF2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ 
+@@ -469,117 +469,117 @@
+ 
+ pxbdsim: $(CPP_OBJS) $(TREE_OBJS) $(BD_SIM_OBJ)
+ 	@echo 'building pxbdsim'
+-	$(CXX) -o "pxbdsim" $(OPT_FLAGS) $(BD_SIM_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxbdsim" $(OPT_FLAGS) $(BD_SIM_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxbdfit: $(CPP_OBJS) $(TREE_OBJS) $(BD_FIT_OBJ)
+ 	@echo 'building pxbdfit'
+-	$(CXX) -o "pxbdfit" $(OPT_FLAGS) $(BD_FIT_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
++	$(CXX) $(CXXFLAGS) -o "pxbdfit" $(OPT_FLAGS) $(BD_FIT_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxnni: $(CPP_OBJS) $(TREE_OBJS) $(NNI_OBJ)
+ 	@echo 'building pxnni'
+-	$(CXX) -o "pxnni" $(OPT_FLAGS) $(NNI_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
++	$(CXX) $(CXXFLAGS) -o "pxnni" $(OPT_FLAGS) $(NNI_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxlstr: $(CPP_OBJS) $(TREE_OBJS) $(LS_TR_OBJ)
+ 	@echo 'building pxlstr'
+-	$(CXX) -o "pxlstr" $(OPT_FLAGS) $(LS_TR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxlstr" $(OPT_FLAGS) $(LS_TR_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxmrca: $(CPP_OBJS) $(TREE_OBJS) $(MRCA_OBJ)
+ 	@echo 'building pxmrca'
+-	$(CXX) -o "pxmrca" $(OPT_FLAGS) $(MRCA_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxmrca" $(OPT_FLAGS) $(MRCA_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxmrcacut: $(CPP_OBJS) $(TREE_OBJS) $(MRCACUT_OBJ)
+ 	@echo 'building pxmrcacut'
+-	$(CXX) -o "pxmrcacut" $(OPT_FLAGS) $(MRCACUT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxmrcacut" $(OPT_FLAGS) $(MRCACUT_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxmrcaname: $(CPP_OBJS) $(TREE_OBJS) $(MRCANAME_OBJ)
+ 	@echo 'building pxmrcaname'
+-	$(CXX) -o "pxmrcaname" $(OPT_FLAGS) $(MRCANAME_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxmrcaname" $(OPT_FLAGS) $(MRCANAME_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxcltr: $(CPP_OBJS) $(TREE_OBJS) $(CLTR_OBJ)
+ 	@echo 'building pxcltr'
+-	$(CXX) -o "pxcltr" $(OPT_FLAGS) $(CLTR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxcltr" $(OPT_FLAGS) $(CLTR_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxt2new: $(CPP_OBJS) $(TREE_OBJS) $(T2NEW_OBJ)
+ 	@echo 'building pxt2new'
+-	$(CXX) -o "pxt2new" $(OPT_FLAGS) $(T2NEW_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxt2new" $(OPT_FLAGS) $(T2NEW_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxt2nex: $(CPP_OBJS) $(TREE_OBJS) $(T2NEX_OBJ)
+ 	@echo 'building pxt2nex'
+-	$(CXX) -o "pxt2nex" $(OPT_FLAGS) $(T2NEX_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxt2nex" $(OPT_FLAGS) $(T2NEX_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrr: $(CPP_OBJS) $(TREE_OBJS) $(RR_OBJ)
+ 	@echo 'building pxrr'
+-	$(CXX) -o "pxrr" $(OPT_FLAGS) $(RR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrr" $(OPT_FLAGS) $(RR_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxmono: $(CPP_OBJS) $(TREE_OBJS) $(MONO_OBJ)
+ 	@echo 'building pxmono'
+-	$(CXX) -o "pxmono" $(OPT_FLAGS) $(MONO_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxmono" $(OPT_FLAGS) $(MONO_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrmt: $(CPP_OBJS) $(TREE_OBJS) $(RMT_OBJ)
+ 	@echo 'building pxrmt'
+-	$(CXX) -o "pxrmt" $(OPT_FLAGS) $(RMT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrmt" $(OPT_FLAGS) $(RMT_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxtrt: $(CPP_OBJS) $(TREE_OBJS) $(TRT_OBJ)
+ 	@echo 'building pxtrt'
+-	$(CXX) -o "pxtrt" $(OPT_FLAGS) $(TRT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtrt" $(OPT_FLAGS) $(TRT_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrmk: $(CPP_OBJS) $(TREE_OBJS) $(RMK_OBJ)
+ 	@echo 'building pxrmk'
+-	$(CXX) -o "pxrmk" $(OPT_FLAGS) $(RMK_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrmk" $(OPT_FLAGS) $(RMK_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxlog: $(CPP_OBJS) $(TREE_OBJS) $(LOGMANIP_OBJ)
+ 	@echo 'building pxlog'
+-	$(CXX) -o "pxlog" $(OPT_FLAGS) $(LOGMANIP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxlog" $(OPT_FLAGS) $(LOGMANIP_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxtscale: $(CPP_OBJS) $(TREE_OBJS) $(RESCALE_TREE_OBJ)
+ 	@echo 'building pxtscale'
+-	$(CXX) -o "pxtscale" $(OPT_FLAGS) $(RESCALE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtscale" $(OPT_FLAGS) $(RESCALE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 	
+ pxtcol: $(CPP_OBJS) $(TREE_OBJS) $(TCOL_OBJ)
+ 	@echo 'building pxtcol'
+-	$(CXX) -o "pxtcol" $(OPT_FLAGS) $(TCOL_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtcol" $(OPT_FLAGS) $(TCOL_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxtcomb: $(CPP_OBJS) $(TREE_OBJS) $(TCOMB_OBJ)
+ 	@echo 'building pxtcomb'
+-	$(CXX) -o "pxtcomb" $(OPT_FLAGS) $(TCOMB_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtcomb" $(OPT_FLAGS) $(TCOMB_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxtgen: $(CPP_OBJS) $(TREE_OBJS) $(TGEN_OBJ)
+ 	@echo 'building pxtgen'
+-	$(CXX) -o "pxtgen" $(OPT_FLAGS) $(TGEN_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxtgen" $(OPT_FLAGS) $(TGEN_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxpoly: $(CPP_OBJS) $(TREE_OBJS) $(POLY_OBJ)
+ 	@echo 'building pxpoly'
+-	$(CXX) -o "pxpoly" $(OPT_FLAGS) $(POLY_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxpoly" $(OPT_FLAGS) $(POLY_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxcolt: $(CPP_OBJS) $(TREE_OBJS) $(COLLAPSE_TREE_OBJ)
+ 	@echo 'building pxcolt'
+-	$(CXX) -o "pxcolt" $(OPT_FLAGS) $(COLLAPSE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxcolt" $(OPT_FLAGS) $(COLLAPSE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxbp: $(CPP_OBJS) $(TREE_OBJS) $(BP_OBJ)
+ 	@echo 'building pxbp'
+-	$(CXX) -o "pxbp" $(OPT_FLAGS) $(BP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxbp" $(OPT_FLAGS) $(BP_OBJ) $(CPP_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ 
+@@ -587,22 +587,22 @@
+ 
+ pxrls: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RELABEL_SEQ_OBJ)
+ 	@echo 'building pxrls'
+-	$(CXX) -o "pxrls" $(OPT_FLAGS) $(RELABEL_SEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrls" $(OPT_FLAGS) $(RELABEL_SEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxrlt: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RELABEL_TREE_OBJ)
+ 	@echo 'building pxrlt'
+-	$(CXX) -o "pxrlt" $(OPT_FLAGS) $(RELABEL_TREE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxrlt" $(OPT_FLAGS) $(RELABEL_TREE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxupgma: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(UPGMA_OBJ)
+ 	@echo 'building pxupgma'
+-	$(CXX) -o "pxupgma" $(OPT_FLAGS) $(UPGMA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxupgma" $(OPT_FLAGS) $(UPGMA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxnj: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(NJ_OBJ)
+ 	@echo 'building pxnj'
+-	$(CXX) -o "pxnj" $(OPT_FLAGS) $(NJ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxnj" $(OPT_FLAGS) $(NJ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(LDFLAGS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ 
+@@ -610,17 +610,17 @@
+ 
+ pxseqgen: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(SEQGEN_OBJ) $(FORT_OBJS)
+ 	@echo 'building pxseqgen'
+-	$(CXX) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
++	$(CXX) $(CXXFLAGS) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxcontrates: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(CONTRATES_OBJ) $(RATE_OBJS)
+ 	@echo 'building pxcontrates'
+-	$(CXX) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
++	$(CXX) $(CXXFLAGS) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS)
+ 	cat man/$@.1.in > man/$@.1
+ 
+ pxstrec: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(STREC_OBJ) #$(FORT_OBJS)
+ 	@echo 'building pxstrec'
+-	$(CXX) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran
++	$(CXX) $(CXXFLAGS) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RATE_OBJS) $(CPPFLAGS) $(LDFLAGS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran
+ 	cat man/$@.1.in > man/$@.1
+ 
+ 
+@@ -628,11 +628,11 @@
+ #removing until fortran update
+ #pxsm0: $(CPP_OBJS) $(RATE_OBJS) $(SM0_OBJ) $(FORT_OBJS)
+ #	@echo 'building pxsm0'
+-#	$(CXX) -o "pxsm0" $(OPT_FLAGS) $(SM0_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(FORT_OBJS) $(CPP_LIBS) -lgfortran
++#	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxsm0" $(OPT_FLAGS) $(SM0_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(FORT_OBJS) $(CPP_LIBS) -lgfortran
+ 
+ #pxsm2a: $(CPP_OBJS) $(RATE_OBJS) $(SM2A_OBJ) $(FORT_OBJS)
+ #	@echo 'building pxsm2a'
+-#	$(CXX) -o "pxsm2a" $(OPT_FLAGS) $(SM2A_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(FORT_OBJS) $(CPP_LIBS) -lgfortran
++#	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o "pxsm2a" $(OPT_FLAGS) $(SM2A_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(FORT_OBJS) $(CPP_LIBS) -lgfortran
+ 
+ 
+ 
diff --git a/debian/patches/i386.patch b/debian/patches/i386.patch
new file mode 100644
index 0000000..50091bc
--- /dev/null
+++ b/debian/patches/i386.patch
@@ -0,0 +1,22 @@
+Description: fix "nan" test failures on i386 caused by -ffast-math
+Author: Étienne Mollier <emollier@debian.org>
+Bug: https://github.com/FePhyFoFum/phyx/issues/145#issuecomment-824866619
+Last-Update: 2022-04-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- phyx.orig/src/Makefile.in
++++ phyx/src/Makefile.in
+@@ -32,7 +32,12 @@
+ endif
+ 
+ ifneq "$(CXX)" "icc"
+-    OPT_FLAGS += -ffast-math -ftree-vectorize
++    OPT_FLAGS += -ftree-vectorize
++    ifneq ($(filter @host_cpu@,i386 i486 i586 i686),)
++        OPT_FLAGS += -ffloat-store
++    else
++        OPT_FLAGS += -ffast-math
++    endif
+ endif
+ 
+ NLOPT_PROGRAMS :=
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..70dd5c1
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+hardening.patch
+build-more-programs.patch
+i386.patch
diff --git a/debian/phyx.logfile b/debian/phyx.logfile
new file mode 100644
index 0000000..e4382ac
--- /dev/null
+++ b/debian/phyx.logfile
@@ -0,0 +1,2 @@
+pxaa2cdn
+pxaa2cdn --help
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..ba3668e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,35 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+ifneq (,$(filter $(DEB_BUILD_ARCH),i386))
+export DEB_CXXFLAGS_MAINT_APPEND += -ffloat-store
+endif
+
+
+%:
+	dh $@ --sourcedirectory=src
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	cd src && python3 run_tests.py
+endif
+
+override_dh_auto_install:
+	mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
+	dh_auto_install -- PREFIX=$(CURDIR)/debian/$(DEB_SOURCE)/usr
+	#echo "#!/usr/bin/python3" > $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+	#cat src/Phyx_Gui.py >> $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+
+override_dh_compress:
+	dh_compress --exclude=.pdf
+
+override_dh_auto_clean:
+	rm -rf src/phyx.logfile
+	if [ -r src/Makefile ]; then \
+	  $(MAKE) -C src distclean; \
+	fi
diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/debian/salsa-ci.yml
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..dfbf82d
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,99 @@
+#!/bin/bash
+
+# Remark: Considere running runtime test suite which is different from
+#         this one which is based on the docs.  If this would be implemented
+#         we should probably ship all example data and doc in a separate
+#         phyx-doc package
+
+set -e
+
+pkg=phyx
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+cd pxaa2cdn_example && echo pxaa2cdn && pxaa2cdn -a ND6_aa.fa -n ND6_nuc.fa -o CDN_aln.fa >/dev/null && cd ..
+
+cd pxbdfit_example && echo pxbdfit && pxbdfit -t bd.tre -m yule >/dev/null && cd ..
+
+# cd pxbdsim_example && echo pxbdsim && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file >/dev/null && cd ..
+
+cd pxboot_example && echo pxboot && pxboot -s Alignment -x 112233 -f 0.50 -o output_of_50_jackknife >/dev/null && cd ..
+
+cd pxboot_example && echo pxboot && pxboot -s Alignment -p parts -o output_of_bootstrap >/dev/null && cd ..
+
+cd pxbp_example && echo pxbp && pxbp -t Tree.tre -o bp_output >/dev/null && cd ..
+
+cd pxcat_example && echo pxcat && pxcat -s *.fas *.fa *.phy -p Parts.txt -o Supermatrix.fa >/dev/null && cd ..
+
+cd pxclsq_example && echo pxclsq && pxclsq -s Alignment -p 0.6 >/dev/null && cd ..
+
+cd pxconsq_example && echo pxconsq && pxconsq -s Alignment >/dev/null && cd ..
+
+cd pxcontrates_example && echo pxcontrates && pxcontrates -c contrates_file.txt -t contrates_tree.tre -a 1 >/dev/null 2>/dev/null && cd ..
+
+cd pxfqfilt_example && echo pxfqfilt && pxfqfilt -s fqfilt_test.fastq -m 10 >/dev/null && cd ..
+
+cd pxlog_example && echo pxlog && pxlog -t *.trees -i >/dev/null && cd ..
+
+cd pxlog_example && echo pxlog && pxlog -t *.trees -b 75 -n 2 -o some_output_filename >/dev/null && cd ..
+
+cd pxlssq_example && echo pxlssq && pxlssq -s Alignment >/dev/null && cd ..
+
+cd pxlstr_example && echo pxlstr && pxlstr -t Tree.tre >/dev/null && cd ..
+
+cd pxmrca_example && echo pxmrca && pxmrca -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
+
+cd pxmrcacut_example && echo pxmrcacut && pxmrcacut -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
+
+cd pxmrcaname_example && echo pxmrcaname && pxmrcaname -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
+
+cd pxnj_example && echo pxnj && pxnj -s Alignment.aln >/dev/null && cd ..
+
+cd pxnw_examples && echo pxnw && pxnw -s Alignment.aln >/dev/null && cd ..
+
+cd pxrecode_example && echo pxrecode && pxrecode -s Nucleotide.fa >/dev/null && cd ..
+
+cd pxrevcomp_example && echo pxrevcomp && pxrevcomp -s Nucleotide.fa >/dev/null && cd ..
+
+cd pxrls_example && echo pxrls && pxrls -s test.fa -c oldnames.txt -n newnames.txt >/dev/null && cd ..
+
+cd pxrlt_example && echo pxrlt && pxrlt -t kingdoms.tre -c kingdoms.oldnames.txt -n kingdoms.newnames.txt >/dev/null && cd ..
+
+cd pxrms_example && echo pxrms && pxrms -s Nucleotide.fa -f taxa_to_delete.txt >/dev/null && cd ..
+
+cd pxrmt_example && echo pxrmt && pxrmt -t rmt_test.tre -n s1,s6,s8 >/dev/null && cd ..
+
+cd pxrr_example && echo pxrr && pxrr -t rr_test.tre -g s1,s2 >/dev/null && cd ..
+
+cd pxs2fa_pxs2phy_pxs2nex_example && \
+   echo pxs2fa && pxs2fa -s Alignment >/dev/null && \
+   echo pxs2phy && pxs2phy -s Alignment >/dev/null && \
+   echo pxs2nex && pxs2nex -s Alignment >/dev/null && \
+   cd ..
+
+cd pxseqgen_example && echo pxseqgen && pxseqgen -t seqgen_test.tre >/dev/null && cd ..
+
+cd pxseqgen_example && echo pxseqgen && pxseqgen -t seqgen_test.tre -o output_alignment -m .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 >/dev/null && cd ..
+
+cd pxsstat_example && echo pxsstat && pxsstat -s Bollback_2002_MBE.fa >/dev/null && cd ..
+
+cd pxstrec_example && echo pxstrec && pxstrec -d test.data.narrow -t test.tre -c config_stmap >/dev/null && cd ..
+
+cd pxsw_example && echo pxsw && pxsw -s Alignment.fa >/dev/null && cd ..
+
+cd pxt2new_example && echo pxt2new && pxt2new -t Tree.nex >/dev/null && cd ..
+
+cd pxtlate_example && echo pxtlate && pxtlate -s Sequence.fa >/dev/null && cd ..
+
+cd pxtscale_example && echo pxtscale && pxtscale -t ultra.tre -s 2.0 >/dev/null && cd ..
+
+cd pxupgma_example && echo pxupgma && pxupgma -s drosophila.aln >/dev/null && cd ..
+
+cd pxvcf2fa_example && echo pxvcf2fa && pxvcf2fa -s vcf_file >/dev/null && cd ..
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..f809f28
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+---
+Archive: GitHub
+Bug-Database: https://github.com/FePhyFoFum/phyx/issues
+Bug-Submit: https://github.com/FePhyFoFum/phyx/issues/new
+Changelog: https://github.com/FePhyFoFum/phyx/tags
+Repository: https://github.com/FePhyFoFum/phyx.git
+Repository-Browse: https://github.com/FePhyFoFum/phyx
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_02387
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b596afd
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts="repacksuffix=+ds,dversionmangle=s%\+ds\d*$%%,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%phyx-$1.tar.gz%" \
+	https://github.com/FePhyFoFum/phyx/tags \
+	(?:.*?/)?v?(\d[\d.]*)\.tar\.gz
author	Andreas Tille <tille@debian.org>	2022-11-15 07:43:33 +0100
committer	Andreas Tille <tille@debian.org>	2022-11-15 07:43:33 +0100
commit	24483f9dd4d792e540196d9e93a9967f9445b3e3 (patch)
tree	184bae4b55de285ce355c7195fa6e8ef6d91d85e
parent	bfbc432891d9a002d9774fe6395c317c7a66ba12 (diff)
parent	8b1e601d225d58d41bcca98ff78648a52bd55cd0 (diff)