Fast statistical alignment

FSA is a multiple sequence alignment program for aligning many proteins or RNAs or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to more reliably identify non-homologous sequences than these other programs, although this increased accuracy comes at the cost of decreased speed.

FSA is currently being used for projects including sequencing new worm genomes and analyzing in vivo transcription factor binding in flies.

Input/Output

This program accepts sequences in FASTA format and outputs alignments in FASTA format or Stockholm format.

References

Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009). "Fast Statistical Alignment". PLoS Computational Biology. 5 (5): e1000392. Bibcode:2009PLSCB...5E0392B. doi:10.1371/journal.pcbi.1000392. PMC 2684580. PMID 19478997. 

External links

• FSA web server
• FSA source code