GSR: Simulator - fastsimcoal2
Attribute | Value |
---|---|
Title | fastsimcoal2 |
Short Description | A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios |
Long Description | While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Different markers, such as DNA sequences, SNPs, STRs (microsatellites) or multi-locus allelic data can be generated under a variety of mutation models (e.g. finite- and infinite-site models for DNA sequences, stepwise or generalized stepwise mutation model for STRs data, infinite-allele model for standard multi-allelic data). fastsimcoal can simulate data in genomic regions with arbitrary recombination rates, thus allowing for recombination hotspots of different intensities at any position. fastsimcoal implements a new approximation to the ancestral recombination graph in the form of sequential Markov coalescent allowing it to very quickly generate genetic diversity for >100 Mb genomic segments. fastsimcoal2 now allows one to estimate demographic parameters from the (joint) site frequency spectrum (SFS) using simulations to compute the expected SFS and a robust method for the maximization of the composite likelihood. |
Version | 2.7.0.9 |
Project Started | 2011 |
Last Release | 1 year, 6 months ago |
Homepage | http://cmpg.unibe.ch/software/fastsimcoal2/ |
Citations | Excoffier L, Foll M, fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios., Bioinformatics, 05-01-2011 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 11-10-2017 (2346 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 | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Standard Coalescent, |
Input | |
Data Type | |
File format | Arlequin, NEXUS, |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | |
File Format | NEXUS, Other, |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, |
Gene Flow | User-defined Matrix, |
Spatiality | |
Life Cycle | |
Mating System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | Varying Recombination Rates, |
Mutation Models | k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites, |
Events Allowed | Varying Demographic Features, |
Other | |
Interface | Command-line, Script-based, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used fastsimcoal2.
2023
Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE, Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges., Ecol Evol, 04-13-2023 [Abstract]
Gilabert A, Rieux A, Robert S, Vitalis R, Zapater MF, Abadie C, Carlier J, Ravigné V, Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa., Ecol Evol, 04-19-2023 [Abstract]