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Protein sequence analysis software


If you are interested in multiple sequence alignment or profile-profile alignment software, I recommend my new program, MUSCLE. MUSCLE produces alignments with accuracy at least as good as T-Coffee, on average, with speeds that are significantly better than CLUSTALW, especially for large numbers of sequences . However, MUSCLE lacks a SATCHMO-like graphical viewer. For viewing, I recommend Marcin Joachimiak's excellent Jevtrace software.

This software is made available at no charge.
By downloading and using the software, you agree to the terms of the license agreement.

License agreement

User guide PDF, 500 kb.
Windows binaries ZIP format, 310 kb
Linux binary gzip format, 440 kb
Source code gzip / tar format, 

Citation for SATCHMO:

Robert C. Edgar and Kimmen Sjolander (2003), SATCHMO: Sequence alignment and tree construction using hidden Markov models, Bioinformatics 19(11), 1404-1411.

Citation for COACH:

Robert C. Edgar and Kimmen Sjolander (2004), COACH: profile-profile alignment of protein families using hidden Markov models, Bioinformatics 20(8):1309-18.