Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep

TL;DR

This paper presents a new distance-based phylogenetic reconstruction algorithm that does not assume branch lengths or tree depth, recovering long and near-leaf edges efficiently with guarantees.

Contribution

It introduces a novel algorithm that reconstructs a forest containing all sufficiently long and close-to-leaf edges without assumptions on branch lengths or depth.

Findings

Recovers all long, near-leaf edges with guarantees

Runs in polynomial time

Does not rely on traditional branch length assumptions

Abstract

We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is guaranteed to contain all edges that are: 1) sufficiently long and 2) sufficiently close to the leaves. How much of the true tree is recovered depends on the sequence length provided. The algorithm is distance-based and runs in polynomial time.