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.
news
16.03.2011
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.
05.04.2011
fastsimcoal has been updated to version 1.1.2 to correct a bug
occurring when more than two migration matrices were defined.
Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time
coalescent
simulator of genomic diversity under arbitrarily complex evolutionary
scenarios Bioinformatics 27: 1332-1334
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