Work

CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics

Year: 2025

Type: article

Abstract: 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. We introduce CompactTree, a lightweight header-only C++ library with a user-friendly Python wrapper for traversing ultra-large trees that can be easily incorporated into other tools. We show that CompactTree is orders of magnitude faster and requires orders of magnitude less memory than existing tree packages. CompactTree is freely accessible as an open source project: https://github.com/niemasd/CompactTree.

Source: Gigabyte

DOI: 10.46471/gigabyte.152

Author: Niema Moshiri

Institution: University of California San Diego

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $350

Funder: University of California, San Diego