{"title":"CompactTree：一个轻量级的仅头文件的c++库和用于超大型系统发育的Python包装器。","authors":"Niema Moshiri","doi":"10.46471/gigabyte.152","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte152"},"PeriodicalIF":0.0000,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921128/pdf/","citationCount":"0","resultStr":"{\"title\":\"CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics.\",\"authors\":\"Niema Moshiri\",\"doi\":\"10.46471/gigabyte.152\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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.</p>\",\"PeriodicalId\":73157,\"journal\":{\"name\":\"GigaByte (Hong Kong, China)\",\"volume\":\"2025 \",\"pages\":\"gigabyte152\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-03-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921128/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"GigaByte (Hong Kong, China)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.46471/gigabyte.152\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"GigaByte (Hong Kong, China)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.46471/gigabyte.152","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics.
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.
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