Phylo-Movies: animating phylogenetic trees from sliding-window analyses

Sliding-window phylogenetic analyses of multiple sequence alignments generate sequences of phylogenetic trees that can reveal phylogenetic conflict along genomes, as can be caused by recombination and other sources; yet, comparing trees across genomic windows remains challenging. Phylo-Movies is a browser-based tool-also available as a standalone desktop application-that 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-Foulds 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.