Abstract
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 efficiency. The aphid package is released under the GPL-3 license, and is freely available for download from CRAN and GitHub (https://github.com/shaunpwilkinson/aphid). Supplementary data are available at Bioinformatics online.
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