Abstract
Computation of Patterson’s D-statistic and its five-taxon derivatives are important phylogenetic methods for the quantification of reticulated evolution, yet are limited in application by the lack of a single, comprehensive program to efficiently perform all necessary calculations from common phylogenetic and population genetic program file formats. To increase accessibility for a broad range of researchers, we present a user-friendly program (COMP-D) that provides flexibility for incorporating heterozygous sites, implements multiple statistical methods, and aggregates results from multiple tests. Program augmentations also facilitate the detection of population-level introgression. COMP-D provides a threefold increase in speed relative to comparable software. It is implemented in C++ and released under the GNU General Public License v3.0. Source code is available for Linux/Mac OS X from: https://github.com/stevemussmann/Comp-D_MPI.
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