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| 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.
| 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:
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.