Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor Interchanges, and Subtree Transfers

TL;DR

This paper introduces faster algorithms for comparing phylogenetic trees by efficiently calculating non-shared edges, and extends approximation methods for subtree transfer distances to trees with arbitrary degrees.

Contribution

It presents the first subquadratic algorithm for non-shared edges and improves NNI distance computation, also extending STT distance approximation to degree-d trees.

Findings

Faster $O(n \, \log n)$ algorithm for non-shared edges.

Improved approximation for NNI distance.

Extended STT distance approximation to arbitrary degree trees.

Abstract

The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest neighbor interchange (NNI) distance. In this paper, we give the first subquadratic-time algorithm for finding the non-shared edges, which are then used to speed up the existing approximating algorithm for the NNI distance from $O(n^2)$ time to $O(n \log n)$ time. Another popular distance metric for phylogenies is the subtree transfer (STT) distance. Previous work on computing the STT distance considered degree-3 trees only. We give an approximation algorithm for the STT distance for degree-$d$ trees with arbitrary $d$ and with generalized STT operations.