{"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/computing-the-probability-of-gene-trees","title":"Computing the probability of gene trees concordant with the species tree in the multispecies coalescent","arxiv_id":"2001.06741","date":"2020-01-18","proceeding":null,"authors":[],"abstract":"The multispecies coalescent process models the genealogical relationships of\ngenes sampled from several species, enabling useful predictions about phenomena\nsuch as the discordance between the gene tree and the species phylogeny due to\nincomplete lineage sorting. Conversely, knowledge of large collections of gene\ntrees can inform us about several aspects of the species phylogeny, such as its\ntopology and ancestral population sizes. A fundamental open problem in this\ncontext is how to efficiently compute the probability of a gene tree topology,\ngiven the species phylogeny. Although a number of algorithms for this task have\nbeen proposed, they either produce approximate results, or, when they are\nexact, they do not scale to large data sets. In this paper, we present some\nprogress towards exact and efficient computation of the probability of a gene\ntree topology. We provide a new algorithm that, given a species tree and the\nnumber of genes sampled for each species, calculates the probability that the\ngene tree topology will be concordant with the species tree. Moreover, we\nprovide an algorithm that computes the probability of any specific gene tree\ntopology concordant with the species tree. Both algorithms run in polynomial\ntime and have been implemented in Python. Experiments show that they are able\nto analyse data sets where thousands of genes are sampled, in a matter of\nminutes to hours.","url_abs":"http://arxiv.org/abs/2001.06741v1","url_pdf":"http://arxiv.org/pdf/2001.06741v1.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":"computing-the-probability-of-gene-trees","repo_url":"https://github.com/truszk/gtprob","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}