{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/treegrafter-phylogenetic-tree-based","title":"TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations","arxiv_id":"1802.07304","date":"2018-02-20","proceeding":null,"authors":[],"abstract":"Summary: TreeGrafter is a new software tool for annotating protein sequences\nusing annotated phylogenetic trees. Cur-rently, the tool provides annotations\nto Gene Ontology terms, and PANTHER protein class, family and subfamily. The\nap-proach is generalizable to any annotations that have been made to internal\nnodes of a reference phylogenetic tree. Tree-Grafter takes each input query\nprotein sequence, finds the best matching homologous family in a library of\npre-calculated, pre-annotated gene trees, and then grafts it to the best\nlocation in the tree. It then annotates the sequence by propagating\nanno-tations from its ancestral nodes in the reference tree. We show that\nTreeGrafter outperforms subfamily HMM scoring for cor-rectly assigning\nsubfamily membership, and that it produces highly specific annotations of GO\nterms based on annotated reference phylogenetic trees. This method will be\nfurther inte-grated into InterProScan, enabling an even broader user\ncom-munity.\n  Availability: TreeGrafter is freely available on the web at\nhttps://github.com/haimingt/TreeGrafting.","url_abs":"http://arxiv.org/abs/1802.07304v1","url_pdf":"http://arxiv.org/pdf/1802.07304v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"treegrafter-phylogenetic-tree-based","repo_url":"https://github.com/haimingt/TreeGrafting","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}