Title

Whole genome phylogenetic tree reconstruction using colored de bruijn graphs

Document Type

Conference Proceeding

Publication Date

7-1-2017

Journal

Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017

Volume

2018-January

DOI

10.1109/BIBE.2017.00-44

Keywords

Algorithm; Colored de Bruijn graph; Phylogenetics; Whole genome sequence

ISBN

9781538613245

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.

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