Welcome to PopSim.
What is PopSim?
Popsim is a Wright-Fisher population genetics simulator.
It was first designed to study Astyanax mexicanus cavefish evolution (see How to cite PopSim section).
How to install PopSim
You need to have the GNU Scientific Library (GSL) installed on your computer to use PopSim.
To install PopSim, just compile it:
gcc *.c -o PopSim -lgsl -lgcblas -lm
How to launch PopSim
To launch PopSim, you need to create a parameters file. All parameters must be filled :
Lines can be commented using a # for each parameter, just write parameter name followed by an = signs and the parameter value ie. param = value
#List of parameters:
- nb_locus: number of locus to be generated (if initial state generated without burning)
- nb_gen: number of generation
- init_gen: number of burning generation
- elabra_gen: number of generation in the “El Abra” population
- bn_gen: number of generations during bottleneck
- labCF_gen: number of lab generation for “CF” pop
- labSF_gen: number of lab generations for “SF” pop
- ancestral_popsize: Effective size of the ancestral population
- texas_popsize: Effective size of the “Texas” population
- elabra_popsize: Effective size of the “El Abra” population
- bn_popsize: Effective population during bottleneck
- cf_popsize: Effective size of the “CF” population
- labCF_popsize: Effective size of the “CF” population in lab
- labSF_popsize: Effective size of the “Texas” and “El Abra” populations in lab
- mutaRate: mutation rate
- migra: Should migration occur between population ? 0: no; 1: yes
- STmr: migration rate from “El Abra” to “Texas” populations
- migrantfish_percST: frequency of “El Abra” population migrating to “Texas”
- TSmr: : migration rate from “Texas” to “El Abra” populations
- migrantfish_percTS: frequency of “Texas” population migrating to “El Abra”
- SCmr: migration rate from “El Abra” to “CF” populations
- migrantfish_percSC: frequency of “El Abra” population migrating to “CF”
- CSmr: migration rate from “CF” to “El Abra” populations
- migrantfish_percCS: frequency of “CF” population migrating to “El Abra”
- CTmr: migration rate from “CF” to “Texas” populations
- migrantfish_percCT: frequency of “CF” population migrating to “Texas”
- TCmr: migration rate from “Texas” to “CF” populations
- migrantfish_percTC: frequency of “Texas” population migrating to “CF”
- resultfile: name of output file before lab evolution
- resultfileLab: name of output after lab evolution
- generatePopInit: How should the ancestral population be generated ? 0: burning 1: Sampling in theoretical distribution (recommanded)
- exportLocusPop: 1: will export derived alleles frequencies at each locus at generation defined by exportLocusPopGene; 0: won’t export
- exportLocusPopGene: At which generation should derived alleles frequencies be exported?
- subGenSF: Number of subgenerations in “El Abra” population
- subGenCF: Number of subgenerations in “CF” population
- subGenTexas: Number of subgenerations in “Texas” population
How to cite PopSim?
If you use PopSim, please cite this paper :
Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish Julien Fumey, Hélène Hinaux, Céline Noirot, Sylvie Rétaux, Didier Casane bioRxiv 094748; doi: https://doi.org/10.1101/094748