Phylo-Movies: Animating Phylogenetic Trees from Sliding-Window Analyses

Abstract

Sliding-window phylogenetic analyses of multiple sequence alignments (MSAs) 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 (SPR) moves and animates these transformations. We illustrate its use in two contexts: localising 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.