I develop and maintain methods (often collaboratively) for population genetic/genomic analyses on my GitHub page. Here are descriptions of some of these methods, and links to download and use them. Feel free to contact me with bug reports/questions.
IMa2pParallelized Isolation with Migration (IM) analyses of haplotypic data to estimate evolutionary demography (effective population sizes, migration rates, and divergence times) of populations. Read our paper on IMa2p, published in Molecular Ecology Resources here. Code is available on my GitHub page here.
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IMGui |
InRelate |
p-MULTICLUSTFast and parallelized estimation of genetic ancestry and allele frequencies from polyploid, multilocus, multi-allelic genomic data under the admixture model. Read more about MULTICLUST here (publication on it is coming soon!).
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MigSelectParallelized framework for the estimation of genomic loci under the effects of selection against migration (genomic islands of speciation), or those under the effects of linked natural selection effects. Read the methods paper here (publication on the parallelized implementation, and applications to genomic data coming soon, but watch this video from Dr. Sethuraman at the SSE meetings to learn more).
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IMa3 |
PPP - PopGen Pipeline PlatformAn end-end implementation of scripts for QC, filtering, performing summary statistics estimation, and model-based estimation of evolutionary histories from population genomic data. This project is still in development, but you can track our updates here and install and work with v1 at the PPP development site.
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