t-coffee_11.00.8cbe486-2_i386.deb


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Description

t-coffee - Multiple Sequence Alignment

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name t-coffee
Package version 11.00.8cbe486
Package release 2
Package architecture i386
Package type deb
Installed size 2.64 KB
Download size 876.15 KB
Official Mirror archive.ubuntu.com
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
alignment. Version 2.00 and higher can mix sequences and structures.
T-Coffee allows the combination of a collection of multiple/pairwise,
global or local alignments into a single model. It can also
estimate the level of consistency of each position within the new
alignment with the rest of the alignments. See the pre-print for more
information
T-Coffee has a special called M-Coffee that makes it possible to combine the
output of many multiple sequence alignment packages. In its published version,
it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
T-Coffee.  A special version has been made for Debian, DM-Coffee, that uses
only free software by replacing Clustal W by Kalign. Using the 8 Methods of
M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
methods if you prefer.

Alternatives

Package Version Architecture Repository
t-coffee_11.00.8cbe486-2_amd64.deb 11.00.8cbe486 amd64 Ubuntu Universe
t-coffee - - -

Requires

Name Value
libc6 >= 2.4
libgcc1 >= 1:3.0
libstdc++6 >= 4.1.1

Download

Type URL
Binary Package t-coffee_11.00.8cbe486-2_i386.deb
Source Package t-coffee

Install Howto

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

Files

Path
/usr/bin/t_coffee
/usr/share/doc/t-coffee/README.Debian
/usr/share/doc/t-coffee/changelog.Debian.gz
/usr/share/doc/t-coffee/copyright
/usr/share/man/man1/t_coffee.1.gz

Changelog

2015-12-22 - Andreas Tille <tille@debian.org>
t-coffee (11.00.8cbe486-2) unstable; urgency=medium
* cme fix dpkg-control
* update debian/copyright
* fix clean target
* compress changelog with '-n' option
* propagate hardening options
* Do not build unused TMalign
* When creating subdirectories in $HOME do not make these world
writable but keep users umask
Closes: #751579
* Drop redundant debian/README.source
* Package builds for all architectures so this
Closes: #631249
(feel free to reopen if tests might keep on failing on armel)
2014-08-16 - Andreas Tille <tille@debian.org>
t-coffee (11.00.8cbe486-1) unstable; urgency=low
[ Charles Plessy ]
* Suggest ncbi-blast+. 
[ Andreas Tille ]
* New upstream version
* debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:
since ncbi-blast++ has renamed some perl scripts according to
Debian policy t-coffee needs to be adapted:
s/legacy_blast\.pl/legacy_blast/
s/blastpgp\.pl/blastpgp/
Closes: #730722
* Move some suggested packages to Recommends since these are recommended
when calling t_coffee --help
* Suggests: fsa (will be packaged soon)
2013-11-27 - Charles Plessy <plessy@debian.org>
t-coffee (10.00.r1613-1) unstable; urgency=low
* New upstream release.
2013-07-14 - Charles Plessy <plessy@debian.org>
t-coffee (9.03.r1318-1) unstable; urgency=low
* New upstream release.
[ Tim Booth ]
* Removed the -doc package as it is empty (Closes: #688630).
docs are no longer in tarball but online:
http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
* Rejigged the rules file to use DH, not CDBS.
* Avoid compressing files under t-coffee-examples
* Remove TMalign binary on clean (should avoid building it at all)
* Fix minor typo flagged by Lintian
[ Charles Plessy ]
* Normalised debian/control with config-model-edit.
* Normalised VCS URLs.
* Using Debhelper 9.
* Complies with Policy 3.9.4.
[Andreas Tille]
* debian/upstream: Single Reference field instead of Reference-*
2012-03-02 - Charles Plessy <plessy@debian.org>
t-coffee (9.02.r1228-2) unstable; urgency=low
* Recommend tm-align instead of distributing local copy
(debian/control, debian/t-coffee.install, Closes: #661516).
2012-02-27 - Charles Plessy <plessy@debian.org>
t-coffee (9.02.r1228-1) unstable; urgency=low
* New upstream release (Closes: #649263).
* Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install)
* Corrected debian/rules as upstream test suite was removed.
* Complies with Policy 3.9.3 (debian/control, no other changes needed).
* Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and
debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream.
2011-06-21 - Charles Plessy <plessy@debian.org>
t-coffee (8.99-1) unstable; urgency=low
* New upstream release in Debian.
* Converted and validated debian/copyright to DEP 5 machine-readable format.
* Using debhelper 8 (debian/control, debian/compat).
* Incremented Standards-Version to reflect conformance with Policy 3.9.2.
(debian/control, no change needed).
* Corrected VCS URLs in debian/control.
* Run upstream tests at build time (debian/rules, debian/README.test).
2011-01-29 - Tim Booth <tbooth@ceh.ac.uk>
t-coffee (8.99-0ubuntu1) lucid; urgency=low
* Rebuild for new upstream release.
* There is no changelog from upstream to read.
2010-11-23 - Tim Booth <tbooth@ceh.ac.uk>
t-coffee (8.97-0ubuntu2) lucid; urgency=low
* New upstream release, changed watch file and auto rebuild using uupdate
* Cleared out old patch - apparently unneeded or else needs total re-write
2010-11-01 - Tim Booth <tbooth@ceh.ac.uk>
t-coffee (8.95-1) lucid; urgency=low
* New upstream version, rebuild by Tim for Bio-Linux/Lucid

See Also

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t1-teams_4.16+nmu1_all.deb Teams -- a PostScript font covering ASCII and basic Cyrillic
t2html_2010.0302+gitbec03e2-2.1_all.deb text to HTML converter implemented in Perl
t2n_0.5-1_i386.deb Simple command-line tool for Lego NXT
t38modem_2.0.0-4build2_i386.deb T.38 Fax over IP pseudo modem
tabble_0.43-3_i386.deb program launcher with tabs for X
tabix_1.2.1-2ubuntu1_i386.deb generic indexer for TAB-delimited genome position files
tableau-parm_0.2.0-4_i386.deb tableau write-blocking bridge query/command utility
tablix2_0.3.5-2ubuntu1_i386.deb Kernel for solving general timetabling problems
tacacs+_4.0.4.27a-1_i386.deb TACACS+ authentication daemon
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tachyon-bin-ogl_0.99~b6+dsx-4_i386.deb Parallel/Multiprocessor Standalone Ray Tracer - with OpenGL display
tachyon-doc_0.99~b6+dsx-4_all.deb Parallel/Multiprocessor Ray Tracing System - reference manual
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