This paper provides several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular b...

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Long-form blog post on The Molecular Ecologist describing the utility and ease of use of poppr

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This primer provides a concise introduction to conducting applied analyses of population genetic data in R, with a special emphasis on non-model populations including clonal or partially clonal organisms. It provides a valuable resource for tackling the nitty-gritty analysis of populations that do not necessarily conform to textbook genetics and might or might not be in Hardy-Weinberg equilibrium....

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