RAMACO is a software tool for computing rare maximal exact matches between multiple sequences. A rare match between k sequences S1,…,Sk is a string that occurs at most ti-times in the sequence Si, where the ti > 0 are user-defined thresholds.
The algorithm implemented in Ramaco is based on enhanced suffix arrays. First, the enhanced suffix array of one of the sequences (the reference sequence) is built and then the other sequences are matched separately against this enhanced suffix array. Second, the resulting pairwise exact matches are combined to multiple exact matches. Ramaco is very fast and space efficient, and can even process sets of mammalian chromosomes.
Please contact Stefan Kurtz, if you are interested to obtain a version.
:: MORE INFORMATION
Ohlebusch, E. and Kurtz, S.
Space efficient computation of rare maximal exact matches between multiple sequences
J. Comp. Biol. 15(4):357-377, 2008.