GSR: Simulator - EvolSimulator
Attribute | Value |
---|---|
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 | 17 years, 7 months ago |
Homepage | http://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 |
Last evaluated | 10-03-2019 (1632 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Haploid DNA Sequence (Mostly for microbial genome evolution, all genomes are haploid), |
Variations | Single Nucleotide Variation, Amino acid variation, |
Simulation Method | Forward-time, |
Input | |
Data Type | |
File format | |
Output | |
Data Type | Genotype 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 Format | Fasta or Fastq, Other (Genbank, ngibws), |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Exponential 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 Flow | Other (Evolsimulator can simulate lateral gene transfer between different microbial lineages.), |
Spatiality | |
Life Cycle | |
Mating System | Random 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 | |
Determinant | Multi-locus, |
Models | Other, |
Recombination | |
Mutation Models | Others (Exchangeability matrix), |
Events Allowed | Population Events (Lineages can go extinct), Varying Genetic Features (Global mutation rates can drift over time), |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, |
Language | C or C++, Perl (Accessory scripts), |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used EvolSimulator.
2019
Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA, Alignment-free inference of hierarchical and reticulate phylogenomic relationships., Brief Bioinform, 03-22-2019 [Abstract]
Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, et al., Benchmarking of alignment-free sequence comparison methods., Genome Biol, 07-25-2019 [Abstract]