debian/0000755000000000000000000000000012224064336007170 5ustar debian/source/0000755000000000000000000000000012224064333010465 5ustar debian/source/format0000644000000000000000000000001412222612050011664 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012224064333010614 5ustar debian/patches/series0000644000000000000000000000000012223555551012025 0ustar debian/rate4site.install0000644000000000000000000000004212223554170012457 0ustar usr/bin/rate4site usr/share/man/* debian/rules0000755000000000000000000000074612222615400010247 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) .PHONY: override_dh_strip override_dh_strip: dh_strip --dbg-package=rate4site-dbg get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs %: dh $@ --parallel --with autotools_dev debian/upstream0000644000000000000000000000113612222612050010742 0ustar Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=rate4site/&component=rate4site/&resolution=--- Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=rate4site/ Reference: Author: Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. Title: Comparison of site-specific rate-inference methods: Bayesian methods are superior. Journal: Mol Biol Evol Year: 2004 Volume: 21 Number: 2 Pages: 1781-1791 DOI: 10.1093/molbev/msh194 PMID: 15201400 URL: http://mbe.oxfordjournals.org/content/21/9/1781.abstract eprint: http://mbe.oxfordjournals.org/content/21/9/1781.full debian/control0000644000000000000000000000317312224063511010571 0ustar Source: rate4site Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan Build-Depends: debhelper (>= 9.0.0), automake, autotools-dev Standards-Version: 3.9.4 Homepage: http://www.tau.ac.il/~itaymay/cp/rate4site.html Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/rate4site Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/rate4site Package: rate4site Architecture: any Pre-Depends: debconf (>= 0.5) Depends: ${shlibs:Depends}, ${misc:Depends} Description: detector of conserved amino-acid sites Rate4Site calculates the relative evolutionary rate at each site using a probabilistic-based evolutionary model. This allows taking into account the stochastic process underlying sequence evolution within protein families and the phylogenetic tree of the proteins in the family. The conservation score at a site corresponds to the site's evolutionary rate. Package: rate4site-dbg Architecture: any Section: debug Depends: rate4site (= ${binary:Version}), ${misc:Depends} Description: debugging symbols for rate4site-dbg Rate4Site calculates the relative evolutionary rate at each site using a probabilistic-based evolutionary model. This allows taking into account the stochastic process underlying sequence evolution within protein families and the phylogenetic tree of the proteins in the family. The conservation score at a site corresponds to the site's evolutionary rate. . This package provides the detached debug symbols for rate4site. debian/changelog0000644000000000000000000000023312224063526011040 0ustar rate4site (3.0.0-1) unstable; urgency=low * Initial release (Closes: #725128). -- Guy Yachdav Mon, 05 Aug 2013 21:06:00 +0200 debian/watch0000644000000000000000000000013512223553423010217 0ustar version=3 opts=pasv ftp://rostlab.org/rate4site//rate4site-([0-9.]+)\.tar\.gz debian uupdate debian/copyright0000644000000000000000000000440112223763262011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: predictprotein Upstream-Contact: Guy Yachdav Source: ftp://rostlab.org/rate4site/ Files: debian/* Copyright: 2013 Guy Yachdav License: GPL-2+ Files: src/phylogeny/getopt.h Copyright: 1989-1994, 1996-1999, 2001 Free Software Foundation, Inc. License: LGPL-2.1+ Files: * Copyright: 2013 Nir Ben-Tal License: GPL-2+ License: LGPL-2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library 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 Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU Lesser General Public License version 2.1 can be found in the file `/usr/share/common-licenses/LGPL-2.1'. License: GPL-2+ 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 2 of the License, or (at your option) any later version. . 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. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/compat0000644000000000000000000000000212222612050010354 0ustar 8