Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

September 01, 2017 · Entered Twilight · 🏛 International Conferences on Biological Information and Biomedical Engineering

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Authors Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement arXiv ID 1709.00164 Category q-bio.PE Cross-listed cs.DS Citations 3 Venue International Conferences on Biological Information and Biomedical Engineering Repository https://github.com/Colelyman/kleuren ⭐ 13 Last Checked 3 months ago

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