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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 


Author  Fanny Perraudeau [aut, cre], James Bullard [aut] 
Date of publication  20171002 11:30:09 UTC 
Maintainer  Fanny Perraudeau <[email protected]> 
License  Artistic2.0 
Version  0.99.0 
Package repository  View on CRAN 
Installation 
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