2024/07/17 by Niema Moshiri · 1 voice
Biochemistry, Genetics and Molecular Biology · Computer Science · Earth and Planetary Sciences · #Genomics and Phylogenetic Studies #Algorithms and Data Compression #Evolution and Paleontology Studies
paper · pdf · doi:10.1101/2024.07.15.603593
openalex publication_date 2024/07/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/14
Abstract Motivation The 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. Results We 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. Availability CompactTree can be accessed at: https://github.com/niemasd/CompactTree Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.