title: seq++: analyzing biological sequences with a range of Markov-related models.
abstract: 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.
authors.affiliation: UMR CNRS 8071 Statistique et Génome, 523 place des Terrasses, 91000 Evry, France. miele@genopole.cnrs.fr
authors.forename: Vincent
authors.initials: V
authors.lastname: Miele
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Bourguignon
authors.forename: David
authors.initials: D
authors.lastname: Robelin
authors.forename: Grégory
authors.initials: G
authors.lastname: Nuel
authors.forename: Hugues
authors.initials: H
authors.lastname: Richard
mesh_terms: D000465:Algorithms; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D017385:Sequence Homology; D012984:Software