GSR: Simulator - PhyloSim
| Attribute | Value |
|---|---|
| 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, 10 months ago |
| Homepage | http://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 ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 01-23-2020 (350 days ago) |
| Author verification | The 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Other (Phyologenetic tree, model parameters, optional root sequence.), |
| File format | NEXUS, Phylip, Other (Phylogenetic trees stored as ape phylo objects.), |
| Output | |
| Data Type | Genotype or Sequence, Mutation (Optional), |
| Sequencing Reads | |
| File Format | Fasta 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 | |
| Determinant | Codon-based, |
| Models | |
| Recombination | |
| Mutation Models | Markov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | R, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, |
No example publication using PhyloSim has been provided.
Please propose new citations if you are aware of publications that use this software.