gphmm: Generalized Pair Hidden Markov Chain Model for Sequence Alignment

Implementation of a generalized pair hidden Markov chain model (GPHMM) that can be used to compute the probability of alignment between two sequences of nucleotides (e.g., a reference sequence and a noisy sequenced read). The model can be trained on a dataset where the noisy sequenced reads are known to have been sequenced from known reference sequences. If no training sets are available default parameters can be used.

Package details

AuthorFanny Perraudeau [aut, cre], James Bullard [aut]
MaintainerFanny Perraudeau <>
Package repositoryView on CRAN
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gphmm documentation built on Oct. 2, 2017, 5:03 p.m.