fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.
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...Coalescent simulations, estimation of the SFS, likelihood computations and its maximization were all done with fastsimcoal2, a modified version of the fastsimcoal program [82]....
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...Also, for these larger sequence lengths and sample sizes, ms is unreliable and crashes [15, 47]....
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...arp) that can then be processed with arlequin or arlsumstat (Excoffier and Lischer 2010) to get distributions of various summary statistics. Additional options of fastsimcoal2 can be specified on the command line (type "fastsimcoal2 -h" for help on command line options). fastsimcoal2 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). fastsimcoal2 can simulate data in genomic regions with arbitrary recombination rates, thus allowing for recombination hotspots of different intensities at any position. fastsimcoal2 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. Compiled versions of fastsimcoal2 for Windows, Linux or Mac Os X are available on http://cmpg.unibe.ch/software/fastsimcoal2 Since fastsimcoal2 output is meant to be interfaced with Arlequin or arlsumstat, the reader may also want to get more information on Arlequin on http://cmpg.unibe.ch/software/arlequin35 Since ver 2.1, fastsimcoal2 can be used to estimate demographic parameters from the (joint) SFS, as described in Excoffier et al. (2013)...
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