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README
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......@@ -14,8 +14,9 @@
# version 12.2 September 9, 2009 #
# version 13.0 July 26, 2010 #
# version 14.0 December 2, 2011 #
# version 14.1 October 17, 2017 #
# #
# Mikita Suyama (mikita@genome.med.kyoto-u.ac.jp) #
# Mikita Suyama (mikita@bioreg.kyushu-u.ac.jp) #
# #
#=================================================================#
......@@ -35,6 +36,9 @@ The resulting codon-based DNA alignment can further be subjected
to the calculation of synonymous (Ks) and non-synonymous (Ka)
substitution rates.
The script is licensed under GPL v2.
#-----------#
# Reference
......@@ -176,7 +180,7 @@ Example:
http://www.bork.embl.de/pal2nal
or
http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi
http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi (not working)
#---------#
......@@ -186,10 +190,10 @@ http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi
If you have any questions or comments, please email me:
Mikita Suyama
Center for Genomic Medicine,
Graduate School of Medicine, Kyoto University,
606-8501 Kyoto, JAPAN
tel: +81 75 753 4383
fax: +81 75 753 4382
email: mikita@genome.med.kyoto-u.ac.jp
Medical Institute of Bioregulation
Kyushu University,
812-8582 Fukuoka, JAPAN
tel: +81 92 642 6384
fax: +81 92 642 6562
email: mikita@bioreg.kyushu-u.ac.jp
debian/README.Debian
View file @ 81d3a292
......@@ -9,3 +9,8 @@ lose its .pl suffix. The answer is most likely "yes", but would require
some synchronisation e.g. with the bioperl developers.
-- Steffen Moeller <steffen_moeller@gmx.de> Tue, 23 Nov 2010 16:18:36 +0100
Updated opinion: The .pl suffix better remains available. There are too
many scrips expecting it.
-- Steffen Moeller <steffen_moeller@gmx.de> Thu, 10 May 2018 01:09:29 +0200
debian/changelog
View file @ 81d3a292
pal2nal (14-1) UNRELEASED; urgency=low
pal2nal (14.1-1) unstable; urgency=low
* Initial release (Closes: #604701)
* New upstream version clarified license.
-- Steffen Moeller <moeller@debian.org> Thu, 10 May 2018 01:05:44 +0200
pal2nal (14-1) UNRELEASED; urgency=low
* Initiated packaging.
-- Steffen Moeller <moeller@debian.org> Tue, 23 Nov 2010 16:18:36 +0100
debian/copyright
View file @ 81d3a292
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: Mikita Suyama <mikita@bioreg.kyushu-u.ac.jp>
Source: http://www.bork.embl.de/pal2nal/distribution/
Source: http://www.bork.embl.de/pal2nal/distribution/ to which upstream has no access, found it on
https://sourceforge.net/projects/sboppetrov/files/pal2nal/pal2nal.v14.1.tar.gz/download
Files: *
Copyright: 2004-2011 Mikita Suyama <mikita@bioreg.kyushu-u.ac.jp>
David Torrents, and Peer Bork and their respective employing institute
License: to_be_clarified
License: GPL-2
Files: debian/*
Copyright: Steffen Moeller <moeller@debian.org> on Tue, 23 Nov 2010 16:18:36 +0100
License: GPL-3+
Copyright: Steffen Moeller <moeller@debian.org>
License: GPL-2
License: GPL-2
This package 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; version 2 of the License.
.
This package 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.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
debian/pal2nal.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
.TH PAL2NAL.PL "1" "November 2010" "pal2nal.pl " "User Commands"
.SH NAME
pal2nal.pl \- manual page for pal2nal.pl
pal2nal.pl \- use insight from protein alignment for nucleotide alignment
.SH SYNOPSIS
.B pal2nal.pl
\fIpep.aln nuc.fasta \fR[\fInuc.fasta\fR...] [\fIoptions\fR]
......
pal2nal.pl
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#!/usr/bin/perl
# pal2nal.pl (c) 2017 Mikita Suyama <mikita@bioreg.kyushu-u.ac.jp>
#
# pal2nal.pl (v14) Mikita Suyama
# #----------------------------------------#
# This script is licensed under GPL v2.0
# #----------------------------------------#
#
#
#
# pal2nal.pl (v14.1) Mikita Suyama
#
# Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options] > output
#
......@@ -56,6 +63,10 @@
# NUC1 GCTTGTGATGAATTTGGTGCTCGTCATG--GGG---TTTTAA
# NUC2 GCGGG-GACGACTGG---GCGTAGCAC---GGGGG-TTTTGA
#
#
# v14.1
# - licensed under GPL v2.0
# 2017/10/17
# v14.
# - NCBI GenBank codon table
# 1 Universal code
......