PhyloSimPhyloSim is 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 the Gillespie algorithm to simulate substitutions, insertions and deletions.
The releases are available from CRAN.
Key features
- Simulation of the evolution of a set of discrete characters with arbitrary states evolving by a continuous-time Markov process with an arbitrary rate matrix.
- Explicit implementations of the most popular substitution models (nucleotide, amino acid and codon substitution models).
- Simulation under the popular models of among-sites rate variation, like the gamma (+G) and invariant sites plus gamma (+I+G) models.
- The possibility to simulate under arbitrarily complex patterns of among-sites rate variation by setting the site specific rates according to any R expression.
- Simulation of one or more separate insertion and/or deletion processes acting on the sequences and which sample the insertion/deletion length from an arbitrary discrete distribution or an R expression (so all the probability distributions implemented in R are rea ...