Work

delimtools : an R package for species delimitation

Year: 2026

Type: article

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.

Source: Genome

DOI: 10.1139/gen-2025-0119

Authors: Pedro S. Bittencourt, Rupert A. Collins, Tomas Hrbek

Institutions: Brazilian Institute of Environment and Renewable Natural Resources, Universidade Federal do Amazonas, Natural History Museum, Trinity University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Funder: Conselho Nacional de Desenvolvimento Científico e Tecnológico

Awards: G1040502324, G5850815296