GSR: Simulator - EvolSimulator

Basic Package Attributes
AttributeValue
Title EvolSimulator
Short Description A simulation test bed for hypotheses of genome evolution
Long Description EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.
Version 2.1.0
Project Started 2006
Last Release 14 years, 2 months ago
Homepagehttp://bioinformatics.org.au/tools/evolsim/
Citations Beiko RG, Charlebois RL, A simulation test bed for hypotheses of genome evolution., Bioinformatics, 04-01-2007 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated10-03-2019 (379 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence (Mostly for microbial genome evolution, all genomes are haploid),
VariationsSingle Nucleotide Variation, Amino acid variation,
Simulation MethodForward-time,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence, Phenotypic Trait (Evolsimulator creates abstract habitats, in which organisms can have differential fitness based on their gene content.), Individual Relationship (Both the complete simulated tree and the tree comprising only extant genomes at the end of the simulation is output),
Sequencing Reads
File FormatFasta or Fastq, Other (Genbank, ngibws),
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesExponential Growth or Decline (Speciation and extinction events happen with a certain probability, up to a maximum population size), Carrying Capacity (Each habitat can be limited in terms of the number of simulated niches it contains.),
Gene FlowOther (Evolsimulator can simulate lateral gene transfer between different microbial lineages.),
Spatiality
Life Cycle
Mating SystemRandom Mating (For lateral gene transfers, random donor-recipient pairs are proposed.), Assortative or Disassortative (Proposed lateral gene transfer events can be favoured if they occur between close relatives),
Fecundity
Natural Selection
DeterminantMulti-locus,
ModelsOther,
Recombination
Mutation ModelsOthers (Exchangeability matrix),
Events AllowedPopulation Events (Lineages can go extinct), Varying Genetic Features (Global mutation rates can drift over time),
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++, Perl (Accessory scripts),
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using EvolSimulator has been provided.

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