{"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/whole-genome-phylogenetic-tree-reconstruction","title":"Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs","arxiv_id":"1709.00164","date":"2017-09-23","proceeding":null,"authors":[],"abstract":"We present kleuren, a novel assembly-free method to reconstruct phylogenetic\ntrees using the Colored de Bruijn Graph. kleuren works by constructing the\nColored de Bruijn Graph and then traversing it, finding bubble structures in\nthe graph that provide phylogenetic signal. The bubbles are then aligned and\nconcatenated to form a supermatrix, from which a phylogenetic tree is inferred.\nWe introduce the algorithms that kleuren uses to accomplish this task, and show\nits performance on reconstructing the phylogenetic tree of 12 Drosophila\nspecies. kleuren reconstructed the established phylogenetic tree accurately,\nand is a viable tool for phylogenetic tree reconstruction using whole genome\nsequences. Software package available at: https://github.com/Colelyman/kleuren","url_abs":"http://arxiv.org/abs/1709.00164v2","url_pdf":"http://arxiv.org/pdf/1709.00164v2.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":"whole-genome-phylogenetic-tree-reconstruction","repo_url":"https://github.com/Colelyman/kleuren","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}