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Bioinformatics Advance Access originally published online on March 17, 2005
Bioinformatics 2005 21(11):2783-2784; 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{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

Summary: The seq++ package offers a reference set of programs and an extensible library to biologists and developers working on sequence statistics. Its generality arises from the ability to handle sequences described with any 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

Contact: miele{at}genopole.cnrs.fr


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