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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.
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 more»
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 more»
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  -run_name S  - more»
t-coffee (8.84-1) unstable; urgency=low * New upstream version -- Andreas Tille <email@example.com more»
Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129 Upstrea more»