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

• Tác giả: Niema Moshiri
• Ngôn ngữ: eng
• Ký hiệu phân loại: 809.008 History and description with respect to kinds of persons
• Thông tin xuất bản: China : GigaByte (Hong Kong, China) , 2025
• Bộ sưu tập: NCBI
• ID: 724962

Tóm tắt

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.