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An R package for the Monte Carlo simulation of sequence evolution

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Version bump.

latest commit 2515966a86
Botond Sipos authored January 10, 2014
Octocat-spinner-32 PAMLdat Added ECM PAML dat files. January 06, 2014
Octocat-spinner-32 RData Relaoded empirical models. January 07, 2014
Octocat-spinner-32 cons_test Added consistency test results for the .Internal-less code. February 06, 2012
Octocat-spinner-32 examples Moved some examples from the PhyloSim cosntrutor documentation September 07, 2012
Octocat-spinner-32 misc Added script to recreate empirical codon models. January 06, 2014
Octocat-spinner-32 pkg Version bump. January 10, 2014
Octocat-spinner-32 .gitignore * .gitignore update. October 27, 2010
Octocat-spinner-32 Alphabet.R Documentation read-through for Alphabet class October 08, 2010
Octocat-spinner-32 AminoAcidMatrices.R Class documentation read-through for AminoAcidMatrices.R October 08, 2010
Octocat-spinner-32 AminoAcidSubst.R Fixed PAMLdat path. January 06, 2014
Octocat-spinner-32 BinarySubst.R Class documentation read-through for BinarySubst.R October 08, 2010
Octocat-spinner-32 BrownianInsertor.R Fixed example line lengths. June 12, 2013
Octocat-spinner-32 COPYING Initial git commit. May 27, 2009
Octocat-spinner-32 COPYLEFT Added GPL v3 file. May 27, 2009
Octocat-spinner-32 CodonAlphabet.R CodonAlphabet is now ordered by the translation table - standard code January 06, 2014
Octocat-spinner-32 CodonModels.R Fix to decrease the runtime of the GY94 example. March 20, 2013
Octocat-spinner-32 CodonSubst.R Doc fix. January 06, 2014
Octocat-spinner-32 ContinuousDeletor.R Class documentation read-through for ContinuousDeletor.R October 08, 2010
Octocat-spinner-32 ContinuousInsertor.R Class documentation read-through for ContinuousInsertor.R October 08, 2010
Octocat-spinner-32 DiscreteDeletor.R Class documentation read-through for DiscreteDeletor.R October 08, 2010
Octocat-spinner-32 DiscreteInsertor.R Class documentation read-through for DiscreteInsertor.R October 08, 2010
Octocat-spinner-32 EmpiricalCodonMatrices.R Added classes handling empirical codon models. January 06, 2014
Octocat-spinner-32 Event.R Fixed example line lengths. June 12, 2013
Octocat-spinner-32 FieldDeletor.R Removed explicit loading of the compoisson package. January 07, 2014
Octocat-spinner-32 GeneralInDel.R Fixed example line lengths. June 12, 2013
Octocat-spinner-32 GeneralSubstitution.R Fixed example line lengths. June 12, 2013
Octocat-spinner-32 Makefile
Octocat-spinner-32 NucleotideModels.R Class documentation read-through for NucleotideModels.R October 08, 2010
Octocat-spinner-32 PSRoot.R updated get<ethodsList.PSRoot in order to be compatible with upcoming December 03, 2012
Octocat-spinner-32 PhyloSim.R Fixed alignment reordering in plotting code. January 10, 2014
Octocat-spinner-32 PopularAlphabets.R Class documentation read-through for PopularAlphabets.R October 08, 2010
Octocat-spinner-32 PopularSequences.R Removed scaleWithOmega. October 11, 2010
Octocat-spinner-32 Process.R Removed clone.PSRoot, using clone.Object instead. January 31, 2012
Octocat-spinner-32 QMatrix.R Class documentation read-through for QMatrix.R October 08, 2010
Octocat-spinner-32 README.md Added GSR link. April 30, 2013
Octocat-spinner-32 Sequence.R Fixed example line lengths. June 12, 2013
Octocat-spinner-32 Site.R * Simplified cumulative rate calculation. October 13, 2010
README.md

Gillespie algorithm

PhyloSim

PhyloSim 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.

PhyloSim was brought to you by the Goldman group from EMBL-EBI.

Catalogued on GSR

Publication

Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment - 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 (+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 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 phylo objects (see the man page of exportStatTree.PhyloSim).

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

Building from source

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

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