GSR: Simulator - PhyloSim

Basic Package Attributes
AttributeValue
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) ... please refer to our documentation for details.
Version 2.0.1
Project Started 2010
Last Release 7 years, 7 months ago
Homepagehttp://www.ebi.ac.uk/goldman-srv/phylosim/
Citations Sipos B, Massingham T, Jordan GE, Goldman N, PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment., BMC Bioinformatics, 04-19-2011 [ Abstract, cited in PMC ]
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Last evaluated01-23-2020 (268 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsAmino acid variation, Insertion and Deletion,
Simulation MethodPhylogenetic,
Input
Data TypeOther (Phyologenetic tree, model parameters, optional root sequence.),
File formatNEXUS, Phylip, Other (Phylogenetic trees stored as ape phylo objects.),
Output
Data TypeGenotype or Sequence, Mutation (Optional),
Sequencing Reads
File FormatFasta or Fastq, Other (Plots in various graphics formats),
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
DeterminantCodon-based,
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites,
Events Allowed
Other
InterfaceScript-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageR,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using PhyloSim has been provided.

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