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

Sliding-window phylogenetic analyses of multiple sequence alignments (MSAs) generate sequences of phylogenetic trees that can reveal recombination and other sources of phylogenetic conflict, 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 subtree migrations and animates these transformations. We demonstrate its utility in two contexts: identifying recombination breakpoints in norovirus genomes, where lineages shift from polymerase-based to capsid-based clustering at the ORF1/ORF2 junction, and detecting rogue taxa that change position across bootstrap replicates. Phylo-Movies complements summary statistics such as Robinson-Foulds distances by showing which lineages move, where they move from, and which new groupings they form. Phylo-Movies is freely available at https://github.com/enesberksakalli/phylo-movies, with a norovirus demonstration video at https://vimeo.com/1162400544, the first rogue taxon example at https://vimeo.com/1162561152, and the second example at https://vimeo.com/1162563101.