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Phylo-Movies is a browser-based tool\u2014also available as a standalone desktop application\u2014that decomposes topological differences between consecutive phylogenetic trees into interpretable rooted subtree prune-and-regraft moves and animates these transformations. We illustrate its use in two contexts: localizing candidate recombination breakpoints in norovirus genomes, where taxa change from polymerase-genotype-associated to capsid-genotype-associated placements at the ORF1\/ORF2 junction, and exploring candidate rogue taxa that change position across bootstrap replicates. Phylo-Movies complements quantitative measures such as Robinson\u2013Foulds distances, split-frequency support values, and rogue-taxon scores by showing which subtrees move and how their source and target placements differ. The animations also provide an intuitive educational tool for teaching and workshops. Phylo-Movies is freely available at https:\/\/enesberksakalli.github.io\/phylo-movies\/, with source code at https:\/\/github.com\/enesBerkSakalli\/phylo-movies, and demonstration videos at https:\/\/vimeo.com\/1199476378, https:\/\/vimeo.com\/1199476382, https:\/\/vimeo.com\/1199476534, https:\/\/vimeo.com\/1199487394, and https:\/\/vimeo.com\/1199495473.<\/jats:p>","DOI":"10.1093\/molbev\/msag194","type":"journal-article","created":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T11:51:15Z","timestamp":1786189875000},"source":"Crossref","is-referenced-by-count":0,"title":["Phylo-Movies: animating phylogenetic trees from sliding-window analyses"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5027-2470","authenticated-orcid":false,"given":"Enes","family":"Sakalli","sequence":"first","affiliation":[{"name":"Max Perutz Labs, Vienna BioCenter , 1030 Vienna ,","place":["Austria"]},{"name":"University of Vienna , Vienna ,","place":["Austria"]},{"name":"Vienna BioCenter PhD Program, A Doctoral School of the University of Vienna and Medical University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"Ludwig Boltzmann Institute for Network Medicine, University of Vienna , Vienna ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0442-3177","authenticated-orcid":false,"given":"Simon","family":"Haendeler","sequence":"additional","affiliation":[{"name":"Digital R&D, Sanofi , 240 Richmond St W, Toronto, ON M5V 2C5 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3366-4458","authenticated-orcid":false,"given":"Arndt","family":"von Haeseler","sequence":"additional","affiliation":[{"name":"Ludwig Boltzmann Institute for Network Medicine, University of Vienna , Vienna ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2311-8592","authenticated-orcid":false,"given":"Heiko A","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Max Perutz Labs, Vienna BioCenter , 1030 Vienna ,","place":["Austria"]},{"name":"University of Vienna , Vienna ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"2026082409562120000_msag194-B1","doi-asserted-by":"publisher","first-page":"8543","DOI":"10.1128\/JVI.00463-07","article-title":"Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form","volume":"81","author":"Abecasis","year":"2007","journal-title":"J Virol"},{"key":"2026082409562120000_msag194-B2","doi-asserted-by":"crossref","unstructured":"Aberer AJ, Krompass D, Stamatakis A. 2013a. 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