MAD roots for large trees

TL;DR

The paper discusses the MAD method for accurately rooting large phylogenetic trees using all pairs of OTUs, introduces an efficient algorithm, and demonstrates its effectiveness on large simulated datasets.

Contribution

It establishes properties of the MAD method and presents a fast, memory-efficient algorithm for large-scale phylogenetic rooting.

Findings

Successfully applied to trees with up to 100,000 OTUs

Calculations complete within minutes on standard hardware

Provides a scalable solution for phylogenetic root estimation

Abstract

The Minimal Ancestral Deviation (MAD) method is a recently introduced procedure for estimating the root of a phylogenetic tree, based only on the shape and branch lengths of the tree. The method is loosely derived from the midpoint rooting method, but, unlike its predecessor, makes use of all pairs of OTUs when positioning the root. In this note we establish properties of this method and then describe a fast and memory efficient algorithm. As a proof of principle, we use our algorithm to determine the MAD roots for simulated phylogenies with up to 100,000 OTUs. The calculations take a few minutes on a standard laptop.