Invariant Based Quartet Puzzling

TL;DR

This paper introduces an invariant-based variation of Quartet Puzzling that reconstructs quartet trees using biological invariants, potentially outperforming traditional maximum likelihood methods under certain conditions.

Contribution

It presents a novel invariant-based approach for quartet tree reconstruction, offering an alternative to maximum likelihood methods in phylogenetics.

Findings

Invariant-based quartet puzzling outperforms likelihood-based methods under certain conditions

The method leverages biological invariants for more accurate tree reconstruction

Potential for improved phylogenetic analysis accuracy

Abstract

Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet Puzzling in which the quartet trees are reconstructed using biologically symmetric invariants. We find that under certain conditions, invariant based quartet puzzling outperforms Quartet Puzzling using maximum likelihood.