|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:
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.