{"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/170808944","title":"Using genotype abundance to improve phylogenetic inference","arxiv_id":"1708.08944","date":"2017-08-29","proceeding":null,"authors":["William S. DeWitt III","Luka Mesin","Gabriel D. Victora","Vladimir N. Minin","Frederick A. Matsen IV"],"abstract":"Modern biological techniques enable very dense genetic sampling of unfolding\nevolutionary histories, and thus frequently sample some genotypes multiple\ntimes. This motivates strategies to incorporate genotype abundance information\nin phylogenetic inference. In this paper, we synthesize a stochastic process\nmodel with standard sequence-based phylogenetic optimality, and show that tree\nestimation is substantially improved by doing so. Our method is validated with\nextensive simulations and an experimental single-cell lineage tracing study of\ngerminal center B cell receptor affinity maturation.","url_abs":"http://arxiv.org/abs/1708.08944v2","url_pdf":"http://arxiv.org/pdf/1708.08944v2.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":"170808944","repo_url":"https://github.com/matsengrp/gctree","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"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}