{"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/inference-of-ancestral-recombination-graphs","title":"Inference of Ancestral Recombination Graphs through Topological Data Analysis","arxiv_id":"1505.05815","date":"2016-07-27","proceeding":null,"authors":[],"abstract":"The recent explosion of genomic data has underscored the need for\ninterpretable and comprehensive analyses that can capture complex phylogenetic\nrelationships within and across species. Recombination, reassortment and\nhorizontal gene transfer constitute examples of pervasive biological phenomena\nthat cannot be captured by tree-like representations. Starting from hundreds of\ngenomes, we are interested in the reconstruction of potential evolutionary\nhistories leading to the observed data. Ancestral recombination graphs\nrepresent potential histories that explicitly accommodate recombination and\nmutation events across orthologous genomes. However, they are computationally\ncostly to reconstruct, usually being infeasible for more than few tens of\ngenomes. Recently, Topological Data Analysis (TDA) methods have been proposed\nas robust and scalable methods that can capture the genetic scale and frequency\nof recombination. We build upon previous TDA developments for detecting and\nquantifying recombination, and present a novel framework that can be applied to\nhundreds of genomes and can be interpreted in terms of minimal histories of\nmutation and recombination events, quantifying the scales and identifying the\ngenomic locations of recombinations. We implement this framework in a software\npackage, called TARGet, and apply it to several examples, including small\nmigration between different populations, human recombination, and horizontal\nevolution in finches inhabiting the Gal\\'apagos Islands.","url_abs":"http://arxiv.org/abs/1505.05815v2","url_pdf":"http://arxiv.org/pdf/1505.05815v2.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":"inference-of-ancestral-recombination-graphs","repo_url":"https://github.com/RabadanLab/TARGet","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"topological-data-analysis","task_name":"Topological Data Analysis"}],"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}