CompactTree: A lightweight header-only C++ library for ultra-large phylogenetics

Abstract

MotivationThe study of viral and bacterial species requires the ability to load and traverse ultra-large phylogenies with tens of millions of tips, but existing tree libraries struggle to scale to these sizes. ResultsWe introduce CompactTree, a lightweight header-only C++ library for traversing ultra-large trees that can be easily incorporated into other tools, and we show that it is orders of magnitude faster and requires orders of magnitude less memory than existing tree packages. AvailabilityCompactTree can be accessed at: https://github.com/niemasd/CompactTree Contactniema@ucsd.edu Supplementary informationSupplementary data are available at Bioinformatics online.