Phylo-Movies

Phylo-Movies computes and visualizes subtree-prune-and-regraft transition frames between consecutive phylogenetic trees to reveal taxon and subtree movements across ordered tree series.

Key Features:

• SPR Transition Computation: Decomposes topological differences between consecutive phylogenetic trees into interpretable subtree migrations using subtree-prune-and-regraft moves.
• Tree Animation: Animates SPR transformations between trees to show which lineages move, where they move from, and which new groupings they form.
• Sliding-Window Analysis Support: Processes ordered phylogenetic tree series generated from multiple sequence alignment sliding-window analyses.
• Bootstrap Replicate Analysis: Detects rogue taxa that change position across bootstrap replicates.
• Tree Comparison: Complements Robinson-Foulds distances by visualizing specific lineage movements rather than relying solely on summary statistics.
• MSA Context Integration: Displays multiple sequence alignment context alongside phylogenetic trees.
• Metadata Coloring: Applies coloring based on metadata for visual differentiation of taxa and groupings.
• SPR-Move Analytics: Provides analytical metrics for subtree-prune-and-regraft operations between trees.
• Movie Export: Exports animations as video recordings for presentation and documentation purposes.
• Image Export: Generates static image exports of tree visualizations and comparisons.

Scientific Applications:

• Recombination Detection: Identifies recombination breakpoints in viral genomes, such as the shift from polymerase-based to capsid-based clustering at the ORF1/ORF2 junction in norovirus genomes.
• Rogue Taxon Identification: Detects taxa that exhibit unstable phylogenetic positions across bootstrap replicates or windowed analyses.
• Phylogenetic Conflict Visualization: Reveals sources of phylogenetic conflict across genomic windows in multiple sequence alignments.
• Curated Tree-Series Comparison: Supports comparison of ordered phylogenetic tree series from curated datasets and analytical workflows.

Methodology:

Phylo-Movies decomposes topological differences between consecutive phylogenetic trees into subtree-prune-and-regraft moves and interpolates these transformations to generate animated transition frames.