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.
Recommended Citation
Lyman, C., Fujimoto, M., Suvorov, A., Bodily, P., Snell, Q., Crandall, K., Bybee, S., & Clement, M. (2017). Whole genome phylogenetic tree reconstruction using colored de bruijn graphs. Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017, 2018-January (). http://dx.doi.org/10.1109/BIBE.2017.00-44