fastsimcoal specifications

Information


Unique identifier OMICS_06854
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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fastsimcoal articles

fastsimcoal citations

 (3)
2018
PMCID: 5927459

[…] history, assuming a within-host pathogen population size of 1000 and using fastsimcoal2 [43] to simulate pathogen coalescent, recombination and mutation with scenario-dependent parameters. fastsimcoal2 is an approximate coalescent simulator implementing the sequential markov coalescent model [50, 51] with cross-over recombination. this model describes viral recombination […]

2017
PMCID: 5389967

[…] model for the same number of snps as in the original dataset. we performed parameter estimation for 150 of these pseudo-observed datasets to infer ci. coalescence simulations were performed using fastsimcoal2.5 (excoffier and foll, 2011). we further checked whether our model fit the observed data by sampling parameters from the 95% ci range for 10,000 simulations and comparing observed […]

2016
PMCID: 4928843

[…] may not detect admixture events that happened before the split of the sympatric species. to overcome these limitations and furthermore infer the demographic history of the radiations we used fastsimcoal2 to perform coalescent simulations in pre-defined models and evaluated their fit against our empirical data summarized in the multi-dimensional site frequency spectrum (sfs) [66, 67]. […]

fastsimcoal institution(s)
Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
fastsimcoal funding source(s)
Swiss SNF (grant no. 3100A0-126074)

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