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simuPOP specifications


Unique identifier OMICS_07257
Name simuPOP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for simuPOP

simuPOP citations


The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation

Ecol Evol
PMCID: 5838063
PMID: 29531706
DOI: 10.1002/ece3.3872

[…] portional to their fitness. All simulations were carried out using Python scripts (available at that utilize objects and functions contained within the simuPOP environment (Peng & Kimmel, ). […]


Orion: Detecting regions of the human non coding genome that are intolerant to variation using population genetics

PLoS One
PMCID: 5552289
PMID: 28797091
DOI: 10.1371/journal.pone.0181604

[…] We simulated genomic data using SimuPOP [], a forward-time population genetics simulator in order to test the correlation of different scoring formulations with applied selective pressures. Using SimuPOP's script to simulate rare va […]


Developing approaches for linear mixed modeling in landscape genetics through landscape‐directed dispersal simulations

Ecol Evol
PMCID: 5468135
PMID: 28616172
DOI: 10.1002/ece3.2825

[…] We used pairwise resistance matrices to simulate dispersal between population groupings for sage‐grouse and foxsnakes using simuPOP (Peng & Amos, ; Peng & Kimmel, ) modules in Python 2.7.2. For each resistance surface, the pairwise dispersal (Dispij; proportion of migrants between populations) between populations was deriv […]


Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Ecol Evol
PMCID: 5395429
PMID: 28428839
DOI: 10.1002/ece3.2844

[…] ultiple test correction (Table , gray cells). The AMOVA conducted on the Adriatic–Ionian population samples confirmed the pattern of genetic homogeneity at the basin scale (F ST = 0.00217, p = .4171).SimuPOP forward‐time simulations revealed that, in the case of complete isolation under pure drift, the observed F ST of Adriatic–Ionian population samples can be reached and exceeded in a few generat […]


Negative frequency dependent selection on sympatric mtDNA haplotypes in Drosophila subobscura

PMCID: 5226107
PMID: 28096777
DOI: 10.1186/s41065-016-0020-2

[…] tDNA haplotypes, we conducted a series of Monte-Carlo (MC) simulations of the populations in Oliver et al. []. We used forward-time individual-based simulations in the Python based simulation package simuPOP (version 1.1.1) [] that mimicked the demography and population dynamics in the population cages (see Additional file ). Because we were interested in mtDNA dynamics, we modelled a haploid popu […]


Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Evol Appl
PMCID: 4999531
PMID: 27606009
DOI: 10.1111/eva.12407

[…] entire All Escapee sample. The remaining 99 Teno Escapee were used to estimate allele frequencies for the escapee reference sample. As before, three generations of hybridization were simulated using simuPOP, and NewHybrids used to assign simulated Generation 2 and Generation 3 individuals to different hybrid classes as described above. […]


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simuPOP institution(s)
Department of Statistics, Rice University, Houston, TX, USA

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