zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.
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BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A1, Kristiansen M, Pedersen CN, Mailund T.