TreeKO

TreeKO provides a Python package to compare phylogenetic tree topologies and quantify topological distances while accounting for gene duplication and loss for evolutionary analyses.

Key Features:

• Phylogenetic topology comparison: Computes distances between phylogenetic tree topologies rather than requiring exact and complete mapping of terminal nodes.
• Handling of duplications and losses: Enables comparisons when gene duplication and loss events are present, avoiding arbitrary pruning or exclusion of duplicated trees.
• Recursive pruning algorithm: Uses a recursive algorithm to split gene trees into pruned sub-trees containing only orthologs.
• Aggregated distance computation: Calculates distances based on the aggregated analysis of all pruned tree comparisons.
• Phylome support values: Computes phylome support values for assessing support across gene trees.
• Reconciliation-based measures: Provides reconciliation-based metrics that quantify inferred duplication and loss events.
• Python implementation: Distributed as a Python package for integration into computational workflows.

Scientific Applications:

• Evolutionary analysis of gene families: Quantifies topological differences while accounting for duplication and loss to study gene family evolution.
• Phylome-wide support assessment: Computes phylome support values to evaluate consistency across genome-wide gene trees.
• Genome-scale phylogenetic comparisons: Enables genome-wide comparisons of gene trees in the presence of duplications and losses.
• Orthology-focused analyses: Extracts ortholog-only pruned subtrees to support analyses restricted to orthologous relationships.

Methodology:

Implements a recursive algorithm that splits gene trees into pruned ortholog-only subtrees, aggregates comparisons of all pruned trees to compute topological distances, and computes phylome support values and reconciliation-based measures quantifying inferred duplication and loss events.