visits since March 2011
SIB fastsimcoal University of Berne

fast sequential Markov coalescent simulation of genomic data under complex evolutionary models

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, SNP, STR (microsatellite) 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.


fastsimcoal has been updated to version 1.1.1 to correct a bug in the windows version causing a crash when deme sizes were set to zero (thanks to Stefano Mona for signalling it to us). Mac and Linux versions were apparently unaffected by this bug, but all versions have been updated to 1.1.1.

fastsimcoal has been updated to version 1.1.2 to correct a bug occurring when more than two migration matrices were defined.

downloads (ver 1.1.2)

[windows logo]
Windows 32 bits
[linux logo]
Linux 64 bits
MacOSX 32 bits
MacOSX 64 bits


Comparisons with other coalescent simulations programs such as ms, simcoal2 or MaCS can be found here

getting started

A quick overview of how to get started with fastsimcoal can be found here (but it is better to read the manual first)

bug reports

Send an email to Laurent Excoffier


Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334
Catalogued on GSR

Last updated by L. Excoffier on 05.04.2011
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