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 .


Reference manual

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3.0.5 by Botond Sipos, 10 months ago


Browse source code at https://github.com/cran/phylosim

Authors: Botond Sipos <[email protected]> , Gregory Jordan <[email protected]>

Documentation:   PDF Manual  

Task views:

GPL (>= 3) license

Imports R.methodsS3

Depends on R.oo, ape, compoisson, ggplot2

See at CRAN