simuPOP protocols

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simuPOP specifications

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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 in pipeline

2016
PMCID: 4831444
PMID: 27099711
DOI: 10.1002/ece3.2028

[…] and simulated datasets. for the randomizations, the 126 samples were grouped into three random ‘species' from three random ‘locations' (nine samples total). simulations were performed with simupop version 1.1.4 (peng and kimmel ), considering an island model with nine populations of 1000 individuals each. two scenarios were simulated, one with migration rate m = 0.5 (‘panmictic') […]


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simuPOP in publications

 (32)
PMCID: 5838063
PMID: 29531706
DOI: 10.1002/ece3.3872

[…] to their fitness. all simulations were carried out using python scripts (available at https://github.com/comeaultresearch/simuhybrid) that utilize objects and functions contained within the simupop environment (peng & kimmel, )., loci were equally spaced along each individual's chromosomes. the two pairs of loci that contain epistatically interacting loci (i.e., “epistatic” loci) […]

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

[…] by taking the average of two individual component resistance surfaces., 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 […]

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

[…] 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 […]

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

[…] the subsets of 200, 160, 120, 80 and 40 loci selected for hybrid discrimination., to test whether the 200 snps could in combination be used to discriminate hybrid classes, we used the python package simupop (peng & kimmel, ) to simulate populations with allele frequencies at these snps approximating those observed in our genotyped and/or allelotyped samples (all escapee, old teno mainstem, […]

PMCID: 4938419
PMID: 27392065
DOI: 10.1371/journal.pone.0158216

[…] statistical power and to explore the limits of our bayesian modelling approach, hbm was applied to data simulated under different selection scenarios. simulations were performed using the software simupop [], an individual-based forward simulation of population evolution in python language (http://simupop.sourceforge.net/main/homepage), and figshare doi: 10.6084/m9.figshare.1385219 […]


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

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