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t-coffee

Multiple Sequence Alignment

Variants:
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 also allows to 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.

Homepage:
Package version:8.84-1
Architecture:i386
Distribution:Debian
Filename:t-coffee_8.84-1_i386.deb

/usr/share/doc/t-coffee/README

README for T-Coffee installation version 6.70 and higer

UNIX/LINUX/Mac OSX

T-Coffee requires gcc, g77, makefile, CPAN, an internet connection and your root password	
	

   1. Download and save the Package
   2. gunzip t_coffee.tar.gz
   3. tar -xvf t_coffee.tar
   4. cd T-COFFEE_distribution_Version_X.XX
   5. ./install

This installation procedure is semi-interactive. It will prompt questions h
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/usr/share/doc/t-coffee/README.Debian

T-COFFEE for Debian
-------------------

T-COFFEE comes with a special mode, 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-T, 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 Kali
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/usr/share/man/man1/t_coffee.1.gz

T-COFFEE(1)                                              T-COFFEE(1)



NAME
       t-coffee - multiple sequence alignment

SYNOPSIS
       t_coffee [options]file

       t-coffee aligns multiple DNA or protein sequences.

OPTIONS
       A  summary  of  options  is  included  below.  For a complete
       description, see the documentation.

       -full_log S [0]

       -run_name S [0]

       -
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/usr/share/doc/t-coffee/changelog.Debian.gz

t-coffee (8.84-1) unstable; urgency=low

  * New upstream version

 -- Andreas Tille <tille@debian.o
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/usr/share/doc/t-coffee/copyright

Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
Upstrea
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