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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute


Multiple sequence alignment program for both protein and DNA.

This multiple sequence alignment program is more sophisticated and well regarded than those in most DNA/Protein toolboxes such as DNAStar, GCG, etc. However, it runs in the command line mode on linux systems. It can however handle very large/long alignments and more extensive searches for the best possible alignment.

Multiple Sequence Alignment
Where? How?
T-Coffee is maintained on the emu linux server. It can be run by typing "t_coffee" from any directory.
Last installation and version
The latest installed version is v 2.66 installed on May 27, 2005.
Prior installations available

programs web site
GPL (GNU public license)
Local expertise
IT: Martin Fleming

The program often outputs (depending on settings) an intermediate phylogeny used in making progressively better alignments - not the final phylogeny as a result of the alignment.

Technical Data

  • tested on:
  • emu path: /usr/local/share/t_coffee_2.66/
  • on $PATH? yes​