GSR: Simulator - fastsimcoal

Basic Package Attributes
AttributeValue
Title fastsimcoal
Short Description A continuous-­‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
Long Description Fastsimcoal is a program to generate the neutral genomic molecular diversity in current or ancient samples drawn from a population with a complex demographic history. Fastsimcoal is a completely rewritten version of simcoal2 (Laval and Excoffier, 2004), a coalescent simulation program implementing a generation by generation approach while fastsimcoal is based on a much faster continuous time approximation. Despite a completely new coalescent engine, fastsimcoal uses exactly the same input files as simcoal2, and it produces very similar output files. Fastsimcoal typically generates many replicates of random outcome of molecular diversity under a user-­‐defined evolutionary scenario. The evolutionary scenario is defined in an input parameter file (extension .par) and the output diversity is written in arlequin project files (extension .arp) that can then be processed with arlequin or arlsumstat (Excoffier and Lischer, 2010) to get distributions of various summary statistics. Additional options of fastsimcoal can be specified on the command line (type "fastsimcoal -­‐h" for help on command line options). 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.
Version 1.1.2
Project Started 2011
Last Release 9 years, 6 months ago
Homepagehttp://cmpg.unibe.ch/software/fastsimcoal/
Citations Excoffier L, Foll M, fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios., Bioinformatics, 05-01-2011 [ Abstract, cited in PMC ]
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Last evaluated11-10-2017 (1071 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodStandard Coalescent,
Input
Data Type
File formatArlequin, NEXUS,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatNEXUS, Other,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline,
Gene FlowUser-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationVarying Recombination Rates,
Mutation Modelsk-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites,
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Support,

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