PhyloSim

<tt>PhyloSim</tt> is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent <tt>R</tt>. It is built on the top of the R.oo and ape packages and uses the Gillespie algorithm to simulate substitutions, insertions and deletions.

<tt>PhyloSim</tt> was brought to you by the Goldman group from EMBL-EBI.

Publication

Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) <i>PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment</i> - BMC Bioinformatics 12:104 doi:10.1186/1471-2105-12-104

Download an install

The released packages 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 (<tt>+G</tt>) and invariant sites plus gamma (<tt>+I+G</tt>) models.

• The possibility to simulate under arbitrarily complex patterns of among-sites rate variation by setting the site specific rates according to any <tt>R</tt> 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 <tt>R</tt> expression (so all the probability distributions implemented in <tt>R</tt> are readily available for this purpose).

• Simulation of the effects of variable functional constraints over the sites by site-process specific insertion and deletion tolerance parameters which determine the rejection probability of a proposed insertion/deletion.

• The possibility of having a different set of processes and site-process specific parameters for every site, which allows for an arbitrary number of partitions in the simulated data.

• The possibility to evolve sites by a combination of substitution processes along a single branch.

• Simulation of heterotachy and other cases of non-homogeneous evolution by allowing the user to set "node hook" functions altering the site properties at internal nodes.

• The possibility to export the counts of various events ("branch statistics") as <tt>phylo</tt> objects (see the man page of <tt>exportStatTree.PhyloSim</tt>).

• See the man page of the <tt>PhyloSim</tt> class and the package vignette for more features and examples.

Building from source

The package can be built from the source by issuing <tt>make pack</tt> on a <tt>*nix</tt> system. The building process need the standard unix tools, <tt>Perl</tt> and <tt>R</tt> with the <tt>ape</tt>, <tt>R.oo</tt>, <tt>ggplot2</tt> and <tt>compoisson</tt> packages installed.