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Title PhyloSim
Short Description An R package for the Monte Carlo simulation of sequence evolution
Long Description PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Key features of PhyloSim include 1) 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. 2) Explicit implementations of the most popular substitution models (nucleotide, amino acid and codon substitution models). 3) Simulation under the popular models of among-sites rate variation, like the gamma (+G) and invariant sites plus gamma (+I+G) models. 4) The possibility to simulate under arbitrarily complex patterns of among-sites rate variation by setting the site specific rates according to any R expression. 5) 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 readily available for this purpose). 6) 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. 7) 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. 8) The possibility to evolve sites by a combination of substitution processes along a single branch. 9) 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. 10) The possibility to export the counts of various events ("branch statistics") as phylo objects (see the man page of exportStatTree.PhyloSim).
Version 2.0.1
Project Started 2010
Last Release 6 years, 10 months ago
Citations Sipos B, Massingham T, Jordan GE, Goldman N, PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment., BMC Bioinformatics, April 19, 2011 [Abstract, cited in PMC ]
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