clustalw-mpi_0.15-3_amd64.deb


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Description

clustalw-mpi - MPI-distributed global sequence alignment with ClustalW

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Nonfree amd64
Package filename clustalw-mpi_0.15-3_amd64.deb
Package name clustalw-mpi
Package version 0.15
Package release 3
Package architecture amd64
Package type deb
Category field::biology implemented-in::c interface::commandline interface::text-mode non-free/science role::program scope::utility use::comparing works-with-format::plaintext works-with::TODO
Homepage http://www.bii.a-star.edu.sg/achievements/applications/clustalw/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 116.09 KB
Installed size 390.00 KB
ClustalW is a popular tool for multiple sequence alignment. The
alignment is achieved via three steps: pairwise alignment,
guide-tree generation and progressive alignment. ClustalW-MPI is an
MPI implementation of ClustalW. Based on
version 1.82 of the original ClustalW, both the pairwise
and progressive alignments are parallelized with MPI, a
popular message passing programming standard. The
pairwise alignments can be easily parallelized since the many
alignments are time independent on each other. However
the progressive alignments are essentially not parallelizable
because of the time dependencies between each alignment.
Here the recursive parallelism paradigm is applied to the linear space
profile-profile alignment algorithm. This approach is more time
efficient on computers with distributed memory architecture.
Traditional approach that relies on precomputing the profile-profile
score matrix has also been implemented. Results shown the latter is indeed
more appropriate for shared memory multiprocessor computer.
ClustalX is suggested for its support for local realignments, seaview
is a versatile editor of alignments.
The original ClustalW/ClustalX can be found at
URL: http://www.clustal.org/download/pre-2/

Alternatives

Package Version Architecture Repository
clustalw-mpi - - -

Requires

Name Value
libc6 >= 2.7
libhwloc5 -
libopenmpi1.6 -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package clustalw-mpi_0.15-3_amd64.deb
Source Package clustalw-mpi

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install clustalw-mpi deb package:
    # sudo apt-get install clustalw-mpi

Files

Path
/usr/bin/clustalw-mpi
/usr/share/doc/clustalw-mpi/History
/usr/share/doc/clustalw-mpi/README.clustalw-mpi.gz
/usr/share/doc/clustalw-mpi/changelog.Debian.gz
/usr/share/doc/clustalw-mpi/changelog.gz
/usr/share/doc/clustalw-mpi/copyright
/usr/share/doc/clustalw-mpi/examples/db10.input.gz
/usr/share/doc/clustalw-mpi/examples/dele.input.gz
/usr/share/man/man1/clustalw-mpi.1.gz

Changelog

2013-09-08 - Charles Plessy <plessy@debian.org>
clustalw-mpi (0.15-3) unstable; urgency=low
* Removed obsolete DM-Upload-Allowed field.
* Using Debhelper 9.
* Normalised VCS URLs.
* Normalised debian/control using config-model.
* Conforms to Policy 3.9.4.
* Version link to GPL-2 in debian/copyright.
* Escape minus sign in ‘debian/clustalw-mpi.1’.
* Uploaded for openmpi transition (Closes: #722073). 
2012-03-01 - Andreas Tille <tille@debian.org>
clustalw-mpi (0.15-2) unstable; urgency=low
* debian/control:
- Fixed Vcs-Fields
- Updated Standards-Version to 3.9.3 (no changes needed)
- Homepage has changed
- Build-Depends: mpi-default-dev
Closes: #661740
- Depends ${misc:Depends}
- Dropped Build-Depends: cdbs
* debian/source/format: 3.0 (quilt)
* Debhelper compat level 8 (control+compat)
* debian/copyright: Fixed DEP5 issues using
cme fix dpkg-copyright
* deleted debian/README.Debian because there is no point in just
using different words for a package beeing in non-free as it is
just said in debian/copyright
* debian/watch: Deleted because not working
* debian/rules:
- Delete get-orig-source target because not working any more 
because source vanished
- Rewritten using dh
* debian/upstream: bibliographic information
* debian/README.source: document missing source code for current version
2008-07-05 - Charles Plessy <plessy@debian.org>
clustalw-mpi (0.15-1) unstable; urgency=low
* New upstream release.
- Fixes crash when the length of a sequence's name was longer than 60
characters. You must re-define macro MAXNAMES in order to process FASTA
file with sequence names longer than the default length.
* Updated my email address.
* Updated upstreams' email address.
* Refreshed the manpage.
* debian/copyright:
- Lifted debian/copyright to the latest version, and licenced my
contribution to this packaging work to "Same as CLUSTALW-MPI".
- Added a disclaimer clarifying that this package is not part of the
Debian operating system (requirement of Policy 3.8.0).
* debian/patches/01_Makefile.patch removed.
Its function is now carried out by debian/rules and debhelper.
* debian/rules switched to CDBS.
* debian/control:
- Dropped build-dependancy on quilt and added one on cdbs.
- Updated Standards-Version to 3.8.0.
2008-04-06 - Andreas Tille <tille@debian.org>
clustalw-mpi (0.14-1) unstable; urgency=low
[ Andreas Tille ]
* Put package under group maintenance of Debian-Med Team
- DM-Upload-Allowed: Yes
- Vcs tags
- Use correct address as Uploader: Steffen Moeller <moeller@debian.org>
* Switched to quilt
- Move manpage to debian dir and added debian/manpages
- Patched Makefile accordingly
- removed useless t.sh
* Standards-Version: 3.7.3 (no changes needed)
* debhelper >= 5
* Moved Homepage from long description to control fields
* debian/copyright machine readable
* Removed [Biology] from short description
[ Charles Plessy ]
* Bug fix version 0.14 released on Dec 19, 2005.
See /usr/share/doc/clustalw-mpi/History for more details.
* Updated debian/patches for the new upstream version.
* Added myself to the Hall of Fame of debian/copyright
and to the Uploaders in debian/control.
* Updated homepage in debian/copyright and debian/control.
* Added debian/watch file.
* debian/clustalw-mpi.1: incremented version number.
* debian/control:
- Dropped versioned dependencies on lam packages, as they
are satisfied even in Sarge.
- Updated homepage of Clustal.
2005-10-12 - Steffen Moeller <moeller@pzr.uni-rostock.de>
clustalw-mpi (0.13-3) unstable; urgency=low
* Updated lam4 to 7.1.1 (Closes: Bug#329488)
2003-06-30 - Steffen Moeller <moeller@pzr.uni-rostock.de>
clustalw-mpi (0.13-2) unstable; urgency=low
* Updated lam3 to lam4 (Closes: #229939)

See Also

Package Description
cluster3_1.52a-1_amd64.deb Reimplementation of the Eisen-clustering software
conserver-client_8.1.18-2.2_amd64.deb connect to a console server
conserver-server_8.1.18-2.2_amd64.deb connect multiple user to a serial console with logging
context-doc-nonfree_2012.06.27-4_all.deb ConTeXt documentation that is not DFSG free
context-nonfree_2007.03.22-1_all.deb Non-free items from the ConTeXt distribution
coq-doc-html_8.4pl4-1_all.deb documentation for Coq in html format
coq-doc-pdf_8.4pl4-1_all.deb documentation for Coq in pdf format
coq-doc_8.4pl4-1_all.deb documentation for Coq
cpp-4.8-doc_4.8.3-1_all.deb documentation for the GNU C preprocessor (cpp)
cpp-4.9-doc_4.9.1-3_all.deb documentation for the GNU C preprocessor (cpp)
crafty_23.4-6+deb8u1_amd64.deb state-of-the-art chess engine, compatible with xboard
crash-whitepaper_1.0-1.1_all.deb Whitepaper for crash kernel debugging utility
cufflinks_2.2.1-1+b1_amd64.deb Transcript assembly, differential expression and regulation for RNA-Seq
cuneiform-common_1.1.0+dfsg-5_all.deb multi-language OCR system (common)
cuneiform_1.1.0+dfsg-5_amd64.deb multi-language OCR system
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