We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
@InProceedings{wittler:LIPIcs.WABI.2019.2, author = {Wittler, Roland}, title = {{Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {2:1--2:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-123-8}, ISSN = {1868-8969}, year = {2019}, volume = {143}, editor = {Huber, Katharina T. and Gusfield, Dan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.2}, URN = {urn:nbn:de:0030-drops-110325}, doi = {10.4230/LIPIcs.WABI.2019.2}, annote = {Keywords: Phylogenomics, phylogenetics, phylogenetic splits, colored de Bruijn graphs} }
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