GSR: Simulator - SIMCOAL2
Attribute | Value |
---|---|
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 | 19 years, 2 months ago |
Homepage | http://cmpg.unibe.ch/software/simcoal2/ |
Citations |
|
GSR Certification | Accessibility |
Last evaluated | 03-28-2020 (1455 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. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, |
Variations | Biallelic Marker, Single Nucleotide Variation (Can specify minimal allele frequency), Microsatellite, Other (Rflp), |
Simulation Method | Exact Coalescent, |
Input | |
Data Type | |
File format | Arlequin, NEXUS, |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | |
File Format | Arlequin, NEXUS, |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, User Defined, |
Gene Flow | User-defined Matrix, |
Spatiality | |
Life Cycle | |
Mating System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | k-Allele Model, Stepwise Mutation Model, Others, |
Events Allowed | Varying Demographic Features, |
Other | |
Interface | Command-line, Script-based, |
Development | |
Tested Platforms | Windows, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Documentation, Application, |
Number of Primary Citations: 2
Number of Non-Primary Citations: 5
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]