Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests

TL;DR

This paper introduces new fixed-parameter and approximation algorithms for maximum agreement forests in rooted binary phylogenetic trees, improving computational efficiency for understanding reticulate evolution.

Contribution

It presents the first depth-bounded search algorithm for maximum acyclic agreement forests, significantly outperforming previous methods.

Findings

Algorithms outperform previous approaches

First depth-bounded search algorithm for acyclic agreement forests

Improved computational tools for reticulate evolution analysis

Abstract

We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depth-bounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems.