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It embeds phylogenetic trees in the TensorFlow Probability framework, and implements inference algorithms for phylogenetic models given a fixed tree topology. We demonstrate how TreeFlow can be used to quickly implement and assess new models. We also show that it provides reasonable performance for gradient-based inference algorithms compared with specialized computational libraries for phylogenetics.<\/jats:p>","DOI":"10.1093\/sysbio\/syag072","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T11:51:45Z","timestamp":1789041105000},"source":"Crossref","is-referenced-by-count":1,"title":["TreeFlow: Probabilistic Modeling and Automatic Differentiation for Phylogenetics"],"prefix":"10.1093","author":[{"given":"Christiaan","family":"Swanepoel","sequence":"first","affiliation":[{"name":"Centre for Computational Evolution, The University of Auckland , 303\/38 Princes Street, Auckland 1010 ,","place":["New Zealand"]},{"name":"School of Computer Science, The University of Auckland , 303\/38 Princes Street, Auckland 1010 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8153-9822","authenticated-orcid":false,"given":"Mathieu","family":"Fourment","sequence":"additional","affiliation":[{"name":"Australian Institute for Microbiology and Infection, University of Technology Sydney , 5 Broadway, Ultimo, NSW 2007 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Tulane University , 6823 St. Charles Avenue, New Orleans, LA 70118 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hassan","family":"Nasif","sequence":"additional","affiliation":[{"name":"Public Health Sciences Division, Fred Hutchinson Cancer Research Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9818-479X","authenticated-orcid":false,"given":"Marc A","family":"Suchard","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, University of California , 885 Tiverton Drive, Los Angeles, CA 90095 ,","place":["USA"]},{"name":"Department of Computational Medicine, University of California , 885 Tiverton Drive, Los Angeles, CA 90095 ,","place":["USA"]},{"name":"Department of Biostatistics, University of California , 695 Charles E Young Dr. South, Los Angeles, CA 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0607-6025","authenticated-orcid":false,"suffix":"IV","given":"Frederick A","family":"Matsen","sequence":"additional","affiliation":[{"name":"Public Health Sciences Division, Fred Hutchinson Cancer Research Center , 1100 Fairview Ave N, Seattle, WA 98109 ,","place":["USA"]},{"name":"Department of Statistics, University of Washington , Padelford Hall, Northeast Stevens Way, Seattle, WA 98195 ,","place":["USA"]},{"name":"Department of Genome Sciences, University of Washington , 3720 15th Ave NE, Seattle, WA 98195 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexei J","family":"Drummond","sequence":"additional","affiliation":[{"name":"Centre for Computational Evolution, The University of Auckland , 303\/38 Princes Street, Auckland 1010 ,","place":["New Zealand"]},{"name":"School of Biological Sciences, The University of Auckland , 110\/3 Symonds Street, Auckland 1010 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"2026092605312534300_bib1","first-page":"265","article-title":"Tensorflow: a system for large-scale machine learning","volume-title":"Proceedings of the 12th USENIX Conference on Operating Systems Design and Implementation, OSDI\u201916","author":"Abadi","year":"2016"},{"issue":"4","key":"2026092605312534300_bib2","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1007\/BF02498640","article-title":"Model of amino acid substitution in proteins encoded by mitochondrial DNA","volume":"42","author":"Adachi","year":"1996","journal-title":"J. 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