Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis

TL;DR

This paper introduces an efficient distance-based phylogenetic reconstruction algorithm that handles insertions and deletions, achieving polynomial sample complexity and bypassing the need for multiple sequence alignment.

Contribution

It presents a novel alignment-free method with provable polynomial sample complexity for reconstructing phylogenies with insertions and deletions.

Findings

Achieves polynomial sample complexity in the number of taxa.

Bypasses the complex multiple sequence alignment step.

Provides theoretical guarantees for the reconstruction algorithm.

Abstract

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparisons. More importantly, our approach largely bypasses the difficult problem of multiple sequence alignment.