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{{orphan|date=January 2010}}
{{Infobox Software|name=FSA|developer=Robert Bradley ([[UC Berkeley]]), Colin Dewey ([[UW Madison]]), Lior Pachter ([[UC Berkeley]])|latest_release_version=1.5.2|operating_system=[[UNIX]], [[Linux]], [[Apple Macintosh|Mac]]|genre=Bioinformatics tool|licence=Open source}}
'''FSA''' is a [[multiple sequence alignment]] program for aligning many proteins or RNAs or long genomic DNA sequences. Along with [[Multiple Sequence Comparison by Log-Expectation|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.
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