seq++: analyzing biological sequences with a range of Markov-related models.
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.
Miele
Vincent
V
UMR CNRS 8071 Statistique et Génome, 523 place des Terrasses, 91000 Evry, France. miele@genopole.cnrs.fr
Bourguignon
Pierre-Yves
PY
Robelin
David
D
Nuel
Grégory
G
Richard
Hugues
H
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