The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).
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Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.
Genetics. 2015 Dec;201(4):1555-79. doi: 10.1534/genetics.115.181453.