Commit 650b2947 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.2.1

parent bd6ead30
* Clustal Omega:
Fabian Sievers UCD Dublin, Ireland
Andreas Wilm UCD Dublin, Ireland
David Dineen UCD Dublin, Ireland
Johannes Söding Gene Center Munich, Germany
Michael Remmert Gene Center Munich, Germany
* Clustal 2
Mark Larkin UCD Dublin, Ireland
* Clustal 1.X
Toby Gibson EMBL Heidelberg, Germany
Des Higgins UCC Cork, Ireland
Julie Thompson IGBMC Strasbourg, France
* Contributors:
Chenna Ramu EMBL Heidelberg, Germany
Nigel Brown EMBL Heidelberg, Germany
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2012-04-25 Release 1.1.0
DNA and RNA support now added. Sequence type can be specified manually
using --seqtype={Protein|DNA|RNA}
2012-03-27 Release 1.0.4
zipped input now supported
2011-09-07 Release 1.0.3
Bugs fixed:
input failed if first line in fasta file was empty
input failed if Clustal formatted file had trailing residue numbers
'*' character was causing problems, did not get filtered out by squid
--outfmt=fasta was not recognized
'~' gap characters were not recognized in MSF format
amended README re sequence/profile alignment
disallowed empty sequences
doxygen documentation fixes and fix of API example
2011-06-23 Release 1.0.2
2011-06-17 Release 1.0.0 (DeshilHollesEamus)
2010-06-17 Release 0.0.1 (Dubliniensis)
First "release" as program has been able for a while to perform
all basic tasks without problems.
Non-standard features already built-in include:
HMM-iteration (using HMMER for building an HMM) and guide-tree
iteration. On top of that HMM input works fine and
background-frequencies are added to the HHalign process.
Known issues: RNA/DNA alignment is considered buggy. Aligned
sequences have to be dealigned for HHalign to work properly.
The HMMER version message can be ignored if no HMM-iteration
was used.
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# Some useful automake documentation:
# http://www.openismus.com/documents/linux/automake/automake.shtml
# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
# we do not use GNU-style files: NEWS README AUTHORS ChangeLog
#AUTOMAKE_OPTIONS = foreign
ACLOCAL_AMFLAGS=-I m4
SUBDIRS = src
# SUBDIRS = src tests
dist_doc_DATA = README
EXTRA_DIST = Doxyfile
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = clustalo.pc
bug-tests: all
cd bug-tests && $(SHELL) bug-tests.sh;
#dist-hook:
# svnversion . > $(distdir)/src/svnversion.h 2>/dev/null
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IMPORTANT
---------
- consensus output (sto,aln) and compatibilety with bioperl/biopython
- Split Homfam refs in two. Use one part as background HMM, the other parts
for benchmarking
- Implement meta flags:
accurate: --iterations 3
default: --mbed --iterations 1
fast: --mbed
and for more than 10k sequences: --mbed --mbed-iter
- SSE instructions for hhalign (little use in ClustalO frontend; DD)
/
Patch new code which already contains SSE instructions
also fix automake/configure then
- Multi-HMMs; also for Pfam+iteration (FS)
- Show degradation of alignment quality when using x reference sequences
added to y random/false sequences
(Lio Pachter)
- Seed pre-alignment with M-Coffee, MSAProbs, ...
- GUI/API:
Will have to catch/override exits from source.
find . -name \*.c -or -name \*.cpp -or -name \*.h | xargs grep 'exit('
Also best to allow for user override of
void Fatal(char *msg, ...);
void Error(char *msg, ...);
void Warn(char *msg, ...);
void Info(int level, char *msg, ...);
- Soeding: DNA/RNA alignment incl. reading of nucleotide HMMs
- Automatic HMM-selection/search/download for input
- Structure input: Psipred predictions are apparently part of their
hhms and should therefore be ready to use (part automatic
HMM-selection)
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prefix=@prefix@
exec_prefix=@exec_prefix@
libdir=@libdir@
includedir=@includedir@
Name: clustal-omega
Description: @PACKAGE_NAME@ library.
Version: @PACKAGE_VERSION@
Requires:
Libs: -L${libdir} -lclustalo
Cflags: -I${includedir}/clustalo/
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Upstream compilation process does not provide shared library support.
Only static library is available in binary package.
clustalo (1.2.1-2) unstable; urgency=medium
[ Steffen Möller]
* Added debian/upstream/edam
[ Andreas Tille ]
* cme fix dpkg-control
* debian/rules: enable building architecture independent package only
Closes: #806007
* more verbose descriptions
* use linktree to get rid of jquery.js copy
* fix order in debian/copyright
-- Andreas Tille <tille@debian.org> Tue, 24 Nov 2015 17:58:56 +0100
clustalo (1.2.1-1) unstable; urgency=medium
* New upstream version
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* cme fix dpkg-copyright
* use dh-autoreconf
Closes: #744421
-- Andreas Tille <tille@debian.org> Sun, 13 Apr 2014 21:09:34 +0200
clustalo (1.2.0-1) unstable; urgency=low
* New upstream release
* Add DNA/RNA support in description (Closes: #706000).
* Fortify binaries
[Andreas Tille]
- Moved DOI+PMID to References
- BibTeX conform authors
-- Olivier Sallou <osallou@debian.org> Sat, 06 Jul 2013 09:07:37 +0200
clustalo (1.1.0-1) unstable; urgency=low
* New upstream version (DNA/RNA support added)
-- Olivier Sallou <osallou@debian.org> Wed, 02 May 2012 10:56:19 +0200
clustalo (1.0.3-1) unstable; urgency=low
* Initial release (Closes: #652031)
-- Olivier Sallou <olivier.sallou@irisa.fr> Wed, 14 Dec 2011 11:21:56 +0100
.TH clustalo 1 "December 14, 2011" "version 1.0.3" "USER COMMANDS"
.SH NAME
clustalo \- General purpose multiple sequence alignment program for proteins
.SH SYNOPSIS
.B clustalo
[\-h]
.SH DESCRIPTION
Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.
In default mode, users give a file of sequences to be aligned and
these are clustered to produce a guide tree and this is used to guide
a "progressive alignment" of the sequences. There are also facilities
for aligning existing alignments to each other, aligning a sequence to
an alignment and for using a hidden Markov model (HMM) to help guide
an alignment of new sequences that are homologous to the sequences
used to make the HMM. This latter procedure is referred to as
"external profile alignment" or EPA.
Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
package from Johannes Soeding [1]. Guide trees are made using an
enhanced version of mBed [2] which can cluster very large numbers of
sequences in O(N*log(N)) time. Multiple alignment then proceeds by
aligning larger and larger alignments using HHalign, following the
clustering given by the guide tree.
In its current form Clustal-Omega can only align protein sequences but
not DNA/RNA sequences. It is envisioned that DNA/RNA will become
available in a future version.
.PP
.SH USAGE
Tool usage is available in /usr/share/doc/clustalo/README.
.PP
.SH DEVELOPMENT
Headers and libraries are available in libclustalo-dev package.
.SH CITING
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
Remmert M, Söding J, Thompson JD, Higgins DG (2011).
Fast, scalable generation of high-quality protein multiple sequence alignments
using Clustal Omega. Mol Syst Biol 7.
.PP
.SH AUTHOR
Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo
Source: clustalo
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
dh-autoreconf,
dh-linktree,
libargtable2-dev,
doxygen,
graphviz,
sphinx-common
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/clustalo/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/clustalo/trunk/
Homepage: http://www.clustal.org/omega/
Package: clustalo
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
libargtable2-0
Description: General purpose multiple sequence alignment program for proteins
Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for dna/rna/proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.
Package: libclustalo-dev
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
libargtable2-dev,
clustalo (= ${binary:Version})
Suggests: libclustalo-doc
Description: library to embed Clustal Omega
This package contains headers and libraries to include
Clustal Omega in a program. It provides clustal usage
with an API.
Package: libclustalo-doc
Architecture: all
Section: doc
Depends: ${misc:Depends},
${js:Depends}
Description: API documentation for library to embed Clustal Omega
Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for dna/rna/proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.
.
This package contains the HTML documentation to use the Clustal Omega
library provided in package libclustalo-dev.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: clustalo
Source: http://www.clustal.org/omega/
Files: *
Copyright: 2010 UCD Dublin <clustalw@ucd.ie>
License: GPL-2+
Files: src/squid/*
Copyright: 1992-2002 Washington University School of Medicine
License: GPL-2+
Files: debian/*
Copyright: 2011 Olivier Sallou <olivier.sallou@irisa.fr>
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; either version 2 of the License, or
(at your option) any later version.
.
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 <http://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".
Document: clustalo
Title: Clustal Omega API
Author: Generated from Doxygen
Abstract: API for development with clustal omega
Section: Programming/C++
Format: HTML
Index: /usr/share/doc/libclustalo-doc/api/html/index.html
Files: /usr/share/doc/libclustalo-doc/api/html/*
doc/doxygen/html /usr/share/doc/libclustalo-doc/api
replace usr/share/sphinx/themes/basic/static/jquery.js usr/share/doc/libclustalo-doc/api/html/jquery.js
#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
%:
dh $@ --with autoreconf --with linktree
override_dh_auto_build-indep:
# nothing to do here
override_dh_auto_test-indep:
# nothing to do here
override_dh_auto_install-arch:
dh_auto_install -a
rm -rf debian/tmp/usr/lib/pkgconfig
rm -f debian/tmp/usr/lib/*/libclustalo.la
mv debian/tmp/usr/include debian/libclustalo-dev/usr
mv debian/tmp/usr/lib debian/libclustalo-dev/usr
mv debian/tmp/usr/bin debian/clustalo/usr
override_dh_auto_install-indep:
# Generate doxygen doc
mkdir -p doc
doxygen Doxyfile
find doc -name "*.md5" -delete
override_dh_clean:
dh_clean
rm -f _configs.sed
rm -rf doc
topic: topic_0182 Sequence alignment
scope: clustalo
function: operation:0492 Multiple sequence alignment construction
input: data_2044 Sequence
input: format_1927 EMBL format
input: format_1929 FASTA
input: format_1935 gcg
input: format_1936 GenBank format
intut: format_1976 pir
input: format_1948 nbrf
input: format_1997 Phylip format
input: format_2188 UniProt
input: data_3271 Gene tree
input: ??? mBed-like
output: data_1916 Alignment
output: format_1984 FASTA-aln
output: format_1997 Phylip format
output: format_2000 selex
output: format_1961 Stockholm format
output: format_1458 Vienna local RNA secondary structure format
output: data_0872 Phylogenetic tree
output: format_1435 Phylip tree format
Contact: Fabian Sievers (UCD Dublin, Ireland)
Homepage: http://www.clustal.org/omega/
Name: Clustal Omega
Reference:
author: Fabian Sievers and Andreas Wilm and David Dineen and Toby J Gibson and Kevin Karplus and Weizhong Li and Rodrigo Lopez and Hamish McWilliam and Michael Remmert and Johannes Söding and Julie D Thompson and Desmond G Higgins
title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
journal: Molecular Systems Biology
volume: 7
number: 539
year: 2011
PMID: 21988835
DOI: 10.1038/msb.2011.75
URL: http://www.nature.com/msb/journal/v7/n1/full/msb201175.html
# Compulsory line, this is a version 3 file
version=3
http://www.clustal.org/omega/clustal-omega-(.*)\.tar\.gz
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# ===========================================================================
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# LICENSE
#
# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu>
#
# 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, 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
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# with this program. If not, see <http://www.gnu.org/licenses/>.
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# As a special exception, the respective Autoconf Macro's copyright owner
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m4_default([$1], [AC_DEFINE(HAVE_OPENMP,1,[Define if OpenMP is enabled])])
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