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Protocols

fastsimcoal specifications

Information


Unique identifier OMICS_06854
Name fastsimcoal
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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Publications for fastsimcoal

fastsimcoal citations

 (72)
library_books

Bayesian reconstruction of transmission within outbreaks using genomic variants

2018
PLoS Comput Biol
PMCID: 5927459
PMID: 29668677
DOI: 10.1371/journal.pcbi.1006117

[…] basic reproduction number of 1.43, see ); then, we translated the transmission history into a population history, and simulated within-population pathogen coalescent, recombination and mutation with fastsimcoal2 []. Throughout the simulations each host in the outbreak is sampled exactly once. We measure the accuracy of a method as the frequency with which the correct transmission source of each h […]

library_books

Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome wide SNP data

2018
PLoS One
PMCID: 5794058
PMID: 29389966
DOI: 10.1371/journal.pone.0190440

[…] To assess whether genetic clusters displayed evidence of variation in past population sizes, we estimated parameters for a two-epoch demographic model. We used the likelihood framework implemented in fastsimcoal2.5 [, ] which is based on the allele frequency spectrum (AFS). The model included five parameters (three effective population sizes allowed to change at two different times in the past). W […]

call_split

Domestication Origin and Breeding History of the Tea Plant (Camellia sinensis) in China and India Based on Nuclear Microsatellites and cpDNA Sequence Data

2018
Front Plant Sci
PMCID: 5788969
PMID: 29422908
DOI: 10.3389/fpls.2017.02270
call_split See protocol

[…] ARLEQUIN v.3.5 (Exocoffier and Lischer, ), following the method of Sun et al. (). A standard algorithm of the Approximate Bayesian Computing (ABC) toolbox (Wegmann et al., ) and the computer program Fastsimcoal (Exocoffier and Foll, ) was employed. A total of 3 × 106 simulated samples (1 × 106 for each model) were generated to compare the three models. Based on these simulations, a “Bayes-factor” […]

library_books

Evaluating genetic drift in time series evolutionary analysis

2018
J Theor Biol
PMCID: 5703635
PMID: 28958783
DOI: 10.1016/j.jtbi.2017.09.021

[…] either 1% or 10% of the loci.The second batch of Wright–Fisher simulations was based on propagation of genomes with linkage characteristic of Drosophila melanogaster (100 cases in total). The program FastSimCoal (), under a neutral coalescent model, was used to generate the starting genomes, with roughly L=5000 polymorphic positions; 2000 sequences were used in this instance. The propagation of po […]

call_split

Genetic analyses favour an ancient and natural origin of elephants on Borneo

2018
Sci Rep
PMCID: 5772424
PMID: 29343863
DOI: 10.1038/s41598-017-17042-5
call_split See protocol

[…] (i) Microsatellite coalescent simulations.To infer the introduction history of elephants into Borneo, we used fastsimcoal to generate simulated microsatellite data under different demographic scenarios and arlsumstat to calculate summary statistics, coupled together in ABCtoolbox. We defined and parameterized […]

library_books

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

2018
Mol Biol Evol
PMCID: 5905656
PMID: 29346646
DOI: 10.1093/molbev/msy004

[…] Nebraska Sand Hills, we inferred the demographic history of populations based on the joint SFS obtained from the random anonymous genomic regions, using the composite likelihood method implemented in fastsimcoal2 v3.05 (). In particular, we were interested in testing whether the Sand Hills populations were founded widely from across the ancestral range, or whether there was a single colonization e […]

Citations

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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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