GeoMeTree

GeoMeTree computes geodesic distances between phylogenetic trees to quantify evolutionary divergence by finding shortest paths in the space of weighted phylogenetic trees.

Key Features:

• Geodesic Distance Calculation: Computes the geodesic distance, defined as the length of the shortest path between two points in the geometric space of phylogenetic trees.
• Exact Algorithm Implementation: Implements an exact algorithm to calculate geodesic distances between weighted phylogenetic trees.
• Efficiency in Computation: Implementation enables fast computations for practical cases while the algorithm's worst-case running time is exponential.
• Approximation via Cone Path: Provides a cone path approximation that can be computed in linear time and serves as an efficient estimate of the geodesic distance for large or complex trees.

Scientific Applications:

• Metazoan gene-tree analysis: Analyze gene trees across metazoan species to study evolutionary patterns.
• Comparison of phylogenetic hypotheses: Compare phylogenetic hypotheses derived from different datasets or inference methods.
• Robustness assessment of phylogenetic inferences: Investigate the robustness of phylogenetic inferences by quantifying variations in tree structures.

Methodology:

Maps phylogenetic trees into a geometric space and uses an exact algorithm (implemented in Python) to find the shortest path (geodesic) between weighted trees, with an optional cone path linear-time approximation.