GSR: Simulator - SIMCOAL2

Basic Package Attributes
AttributeValue
Title SIMCOAL2
Short Description A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models
Long Description We present here SIMCOAL2, an extended version of the SIMCOAL program (Excoffier et al. 2000), to simulate the neutral genetic diversity at partially linked loci under different histories and a wide range of migration and demographic models. SIMCOAL2 includes a number of new features compared to the previous version: The possibility of arbitrary recombination rates between adjacent loci Multiple coalescent events per generation, allowing the correct simulation of very large samples and very large recombining genomic regions The simulation of SNP data with arbitrary minimum frequency, for instance to simulate ascertainment bias The output of diploid genotypic data generated under the assumption of Hardy-Weinberg equilibrium The simulation of a mixture of different data types (DNA sequence, RFLP, STR, or SNP) along a single chromosome.
Version 2.1.2
Project Started 2000
Last Release 16 years ago
Homepagehttp://cmpg.unibe.ch/software/simcoal2/
Citations
  • Laval G, Excoffier L, SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history., Bioinformatics, 10-12-2004 [ Abstract , cited in PMC ]
  • Excoffier L, Novembre J, Schneider S, SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography., J Hered, 11-01-2000 [ Abstract , cited in PMC ]
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Last evaluated03-28-2020 (286 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 DataGenotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation (Can specify minimal allele frequency), Microsatellite, Other (Rflp),
Simulation MethodExact Coalescent,
Input
Data Type
File formatArlequin, NEXUS,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatArlequin, NEXUS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, User Defined,
Gene FlowUser-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates,
Mutation Modelsk-Allele Model, Stepwise Mutation Model, Others,
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsWindows,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

The following 5 publications are selected examples of applications that used SIMCOAL2.

2020

Victoriano PF, Muñoz-Ramírez CP, Canales-Aguirre CB, Jara A, Vera-Escalona I, Burgos-Careaga T, Muñoz-Mendoza C, Habit EM, Contrasting evolutionary responses in two co-distributed species of <i>Galaxias</i> (Pisces, Galaxiidae) in a river from the glaciated range in Southern Chile., R Soc Open Sci, 07-08-2020 [Abstract]

2019

Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, et al., Population structure, connectivity, and demographic history of an apex marine predator, the bull shark <i>Carcharhinus leucas</i>., Ecol Evol, 09-30-2019 [Abstract]

2018

Sharma R, Goossens B, Heller R, Rasteiro R, Othman N, Bruford MW, Chikhi L, Genetic analyses favour an ancient and natural origin of elephants on Borneo., Sci Rep, 01-17-2018 [Abstract]

Pérez-Pardal L, Sánchez-Gracia A, Álvarez I, Traoré A, Ferraz JBS, Fernández I, Costa V, Chen S, Tapio M, Cantet RJC, et al., Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa., Sci Rep, 12-21-2018 [Abstract]

2017

Rovito SM, Schoville SD, Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders., Heredity (Edinb), 10-01-2017 [Abstract]


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