Biosquid

• afetch(1) retrieve an alignment from an alignment database
• alistat(1) show statistics for a multiple alignment file
• compalign(1) compare two multiple alignments
• compstruct(1) calculate accuracy of RNA secondary structure predictions
• revcomp(1) reverse complement a nucleic acid sequence
• seqsplit(1) split seqs into chunks of defined size and overlap
• seqstat(1) show statistics and format for a sequence file
• sfetch(1) get a sequence from a flatfile database.
• shuffle(1) randomize the sequences in a sequence file
• sindex(1) index a sequence database for sfetch
• sreformat(1) convert sequence file to different format
• stranslate(1) translate a nucleic acid sequence to protein ORFs
• weight(1) calculates sequence weights for an alignment