aphid: an R package for analysis with profile hidden Markov models
Abstract
Summary Hidden Markov models (HMMs) and profile HMMs form an integral part of biological sequence analysis, supporting an ever-growing list of applications. The aphid R package can be used to derive, train, plot, import and export HMMs and profile HMMs in the R environment. Computationally-intensive dynamic programing recursions, such as the Viterbi, forward and backward algorithms are implemented in C++ and parallelized for increased speed and...
Paper Details
Title
aphid: an R package for analysis with profile hidden Markov models
Published Date
Mar 6, 2019
Journal
Volume
35
Issue
19
Pages
3829 - 3830
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