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Bioinformatics Advance Access originally published online on June 9, 2005
Bioinformatics 2005 21(16):3427-3428; doi:10.1093/bioinformatics/bti533
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Published by Oxford University Press 2005

Sarment: Python modules for HMM analysis and partitioning of sequences

Laurent Guéguen

Laboratoire Biométrie et Biologie Évolutive (UMR 5558); (NRS); Univ Lyon 1, 43 bd 11 Nov,69622 Villeurbanne cedex, France

Summary: Sarment is a package of Python modules for easy building and manipulation of sequence segmentations. It provides efficient implementation of usual algorithms for hidden Markov Model computation, as well as for maximal predictive partitioning. Owing to its very large variety of criteria for computing segmentations, Sarment can handle many kinds of models. Because of object-oriented programming, the results of the segmentation are very easy tomanipulate.

Availability: Sarment is available on Linux, UNIX and MacOS X operating systems. It is under GPL license. There are binaries for python2.3 or python2.4, as well as sources, in the website http://pbil.univ-lyon1.fr/software/sarment

Contact: gueguen{at}biomserv.univ-lyon1.fr

Received on February 18, 2005; revised on May 18, 2005; accepted on June 7, 2005

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