License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2019.2
URN: urn:nbn:de:0030-drops-110325
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2019/11032/
Go to the corresponding LIPIcs Volume Portal

Wittler, Roland

Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs

pdf-format:
LIPIcs-WABI-2019-2.pdf (1 MB)

Abstract

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.

BibTeX - Entry

@InProceedings{wittler:LIPIcs:2019:11032,
  author =	{Roland Wittler},
  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 =	{Katharina T. Huber and Dan Gusfield},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2019/11032},
  URN =		{urn:nbn:de:0030-drops-110325},
  doi =		{10.4230/LIPIcs.WABI.2019.2},
  annote =	{Keywords: Phylogenomics, phylogenetics, phylogenetic splits, colored de Bruijn graphs}
}

Keywords: Phylogenomics, phylogenetics, phylogenetic splits, colored de Bruijn graphs
Collection: 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
Issue Date: 2019
Date of publication: 03.09.2019

DROPS-Home | Fulltext Search | Imprint | Privacy Published by LZI