A Fast Algorithm for Computing Geodesic Distances in Tree Space

TL;DR

This paper introduces a polynomial time algorithm for efficiently computing geodesic distances between phylogenetic trees in tree space, facilitating biological comparisons and analyses.

Contribution

It presents a novel, fast algorithm that finds geodesics in tree space, solving a key open problem in phylogenetics.

Findings

Algorithm computes geodesics in polynomial time

Starts with a simple path and iteratively shortens it

Enables efficient comparison of phylogenetic trees

Abstract

Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths is the length of the shortest path between them in the continuous tree space introduced by Billera, Holmes, and Vogtmann. This tree space provides a powerful tool for studying and comparing phylogenetic trees, both in exhibiting a natural distance measure and in providing a Euclidean-like structure for solving optimization problems on trees. An important open problem is to find a polynomial time algorithm for finding geodesics in tree space. This paper gives such an algorithm, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained.