Moshiri Niema
Department of Computer Science & Engineering, UC San Diego, La Jolla, CA 92093, USA.
GigaByte. 2025 Mar 7;2025:gigabyte152. doi: 10.46471/gigabyte.152. eCollection 2025.
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.
对病毒和细菌物种的研究需要具备加载和遍历拥有数千万个末端的超大型系统发育树的能力，但现有的树库在扩展到这些规模时面临困难。我们引入了CompactTree，这是一个轻量级的仅包含头文件的C++库，带有一个用户友好的Python包装器，用于遍历超大型树，并且可以轻松地集成到其他工具中。我们表明，CompactTree比现有的树包快几个数量级，并且所需内存少几个数量级。CompactTree作为一个开源项目可免费获取：https://github.com/niemasd/CompactTree 。
