delimtools: an R package for species delimitation.

Abstract

Single-locus species-delimitation methods using DNA barcoding data have made an important contribution to large scale biodiversity inventories and integrative taxonomy, allowing rapid and repeatable estimates of alpha diversity from huge numbers of individuals. A range of distance-based and tree-based methods now exist to perform these analyses, including ABGD, ASAP, GMYC, and mPTP. However, the outputs of such software are idiosyncratic and difficult to integrate and compare. The R package delimtools offers a platform capable of (1) pre-processing, cleaning, and formatting data; (2) collapsing and summarising haplotype information; (3) executing, parsing, and merging program outputs and species partitions; and (4) tabulating results, and visualizing on a phylogenetic tree. The open-source delimtools package opens up new avenues to scale up and standardize species delimitation analyses, and is available on the CRAN (https://cran.r-project.org/package=delimtools) and GitHub (https://github.com/legalLab/delimtools/) repositories.