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Analysis with profile hidden Markov models

aphid is an R package for the development and application ofhidden Markov models and profile HMMs for biological sequence analysis.Functions are included for multiple and pairwise sequence alignment,model construction and parameter optimization, calculation of conditionalprobabilities (using the forward, backward and Viterbi algorithms),tree-based sequence weighting, sequence simulation, and file import/exportcompatible with theHMMER software package.aphid also includes functions for developing and working withstandard hidden Markov models.

This package was written based on the algorithms described in the bookBiological Sequence Analysisby Richard Durbin, Sean Eddy, Anders Krogh and Graeme Mitchison.This book offers an in depth explanation of hidden Markov models andprofile HMMs for users of all levels of familiarity.Many of the examples and datasets in the package are directly derived from thetext, which serves as a useful primer for this package.

To downloadaphid from CRAN and load the package, run

install.packages("aphid")library("aphid")

To download the development version fromGitHub, first ensure a C/C++ compliler is available and thedevtools R package is installed.Linux users will generally have a compiler installed by default;however Windows users may need to downloadRtools and MacOSX users will need Xcode (note that these are not R packages).Install and load the package by running

devtools::install_github("shaunpwilkinson/aphid",build_vignettes=TRUE) library("aphid")

An overview of the package and its functions can be found by running

?aphid

To view the tutorial, run

vignette("aphid-vignette")

If you experience a problem using this package please feel free toraise it as an issue onGitHub.

This software was developed atVictoria University of Wellingtonwith funding from a Rutherford Foundation Postdoctoral Research Fellowshipaward from the Royal Society of New Zealand.