phylosim: Flexible Simulations of Biological Sequence Evolution

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment <doi:10.1186/1471-2105-12-104>.

Version: 3.0.5
Depends: R (≥ 2.15.2), R.oo (≥ 1.13.0), ape (≥ 2.3), compoisson (≥ 0.3), ggplot2 (≥ 0.9.3)
Imports: R.methodsS3
Published: 2019-11-21
Author: Botond Sipos, Gregory Jordan
Maintainer: Botond Sipos <sbotond at gmail.com>
License: GPL (≥ 3)
URL: https://github.com/bsipos/phylosim
NeedsCompilation: no
CRAN checks: phylosim results

Downloads:

Reference manual: phylosim.pdf
Vignettes: PhyloSim
Package source: phylosim_3.0.5.tar.gz
Windows binaries: r-devel: phylosim_3.0.5.zip, r-devel-gcc8: phylosim_3.0.5.zip, r-release: phylosim_3.0.5.zip, r-oldrel: phylosim_3.0.5.zip
OS X binaries: r-release: phylosim_3.0.5.tgz, r-oldrel: phylosim_3.0.5.tgz
Old sources: phylosim archive

Reverse dependencies:

Reverse depends: pcrcoal

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