Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

TL;DR

This paper introduces kleuren, an assembly-free method that uses Colored de Bruijn Graphs to accurately reconstruct phylogenetic trees from whole genome sequences, demonstrated on Drosophila species.

Contribution

Kleuren is a novel algorithm that leverages Colored de Bruijn Graphs for phylogenetic inference without genome assembly, improving accuracy and efficiency.

Findings

Reconstructed the established phylogenetic tree of 12 Drosophila species.

Achieved accurate phylogenetic reconstruction using whole genome data.

Demonstrated the viability of assembly-free phylogenetic methods.

Abstract

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleuren