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Bioinformatics Advance Access published online on March 17, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti389
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 28, 2004
Revised February 1, 2005
Accepted March 9, 2005

Applications note

seq++: analyzing biological sequences with a range of Markov-related models

Vincent Miele 1*, Pierre-Yves Bourguignon 1, David Robelin 1, Grégory Nuel 1, and Hugues Richard 1

1 UMR CNRS 8071 Statistique et Génome, 523 place des Terrasses, 91000 Evry - France

* To whom correspondence should be addressed.
Vincent Miele, E-mail: miele{at}genopole.cnrs.fr


  Abstract

Summary: The seq++ package offers a reference set of programs and an extensible library to biologists and developers working on sequence statistics. Its genericity arises from the ability of handling sequences described with any kind of alphabet (nucleotides, amino acids, codons and others). seq++ enables sequence modelling with various types of Markov models, including Variable Length Markov models and the newly developed Parsimonious Markov models, all of them potentially phased. Simulation modules are supplied for Monte Carlo methods. Hence, this toolbox allows the study of any biological process which can be described by a series of states taken from a finite set.

Availability: Under the GNU General Public Licence at http://stat.genopole.cnrs.fr/seqpp.


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