aphid

Analysis with Profile Hidden Markov Models

Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).

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Description file content

Package
aphid
Type
Package
Title
Analysis with Profile Hidden Markov Models
Version
1.3.1
Author
Shaun Wilkinson [aut, cre]
Maintainer
Shaun Wilkinson
Description
Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
License
GPL-3
URL
BugReports
http://github.com/shaunpwilkinson/aphid/issues
LazyData
TRUE
Encoding
UTF-8
SystemRequirements
GNU make
Depends
R(>= 3.0.0)
Imports
graphics, openssl, kmer (>= 1.0.0), Rcpp (>= 0.12.5), stats
Suggests
ape (>= 4.0), knitr, rmarkdown, testthat
LinkingTo
Rcpp
VignetteBuilder
knitr
RoxygenNote
6.1.0
NeedsCompilation
yes
Packaged
2018-11-10 01:23:41 UTC; shaun
Repository
CRAN
Date/Publication
2018-11-10 05:50:03 UTC

install.packages('aphid')

1.3.1

a month ago

http://github.com/shaunpwilkinson/aphid

Shaun Wilkinson

GPL-3

Depends on

R(>= 3.0.0)

Imports

graphics, openssl, kmer (>= 1.0.0), Rcpp (>= 0.12.5), stats

Suggests

ape (>= 4.0), knitr, rmarkdown, testthat

Discussions