fastsimcoal

Basic Package Attributes
Attribute	Value
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	7 years ago
Homepage	http://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, May 1, 2011 [Abstract, cited in PMC ]
GSR Certification	✔Accessibility ✔Documentation ✘Application ✔Support
Last certified	June 1, 2015 (1039 days ago)
Author verification	The 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 Category	Attribute
Target
Type of Simulated Data	Haploid DNA Sequence,
Sequencing Reads
Variations	Biallelic Marker, Single Nucleotide Variation,
Simulation Method	Standard Coalescent,
Input
Data Type
File format	Arlequin, NEXUS,
Output
Data Type	Genotype or Sequence,
Sequencing Reads
File Format	NEXUS, Other,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes	Constant Size , Exponential Growth or Decline,
Gene Flow	User-defined Matrix,
Life Cycle
Mating System	Random Mating,
Fecundity
Natural Selection
Determinant
Models
Recombination	Varying Recombination Rates,
Mutation Models	k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites,
Events Allowed	Varying Demographic Features,
Other
Interface	Command-line, Script-based,
Development
Tested Platforms	Windows, Mac OS X, Linux and Unix,
Language	C or C++,
License	GNU Public License,
GSR Certification	Accessibility, Documentation, Support,

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