t-coffee - Multiple Sequence Alignment

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.



    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


    • /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


    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