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Bioinformatics Advance Access published online on June 9, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti533
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 18, 2005
Revised May 18, 2005
Accepted June 7, 2005

Applications note

Sarment: Python modules for HMM analysis and partitioning of sequences

Laurent Guéguen 1*

1 UMR CNRS 5558 - Laboratoire Biométrie et Biologie Évolutive, Université Claude Bernard - Lyon I, 69622 Villeurbanne cedex FRANCE

* To whom correspondence should be addressed.
Laurent Guéguen, E-mail: gueguen{at}biomserv.univ-lyon1.fr


  Abstract

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

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


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