MutationOrder (hackage): Determine the most likely order in which single nucleotide mutations happened between two RNA sequences.  Developed to analyse the HAR 1 region, but agnostic to the actual sequences and can be used to analyze any RNA sequence that fits the algorithmic constraints.  As long as the two input RNAs are small enough enough (couple hundred nucleotides) and the number of mutations is small enough (around 20-26, since the algorithm is exponential in this number) the algorithm should work for similar problems without changes.  We currently only consider point mutations, not in-dels.
Keywords: bioinformatics|gpl|library|program