Alignment- and reference-free phylogenomics with colored de Bruijn graphs

Wittler R (2020)
Algorithms for Molecular Biology 15(1): 4.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. Results We present a new whole-genome based approach to infer 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. Conclusions The introduced new methodology for large-scale phylogenomics shows high potential. 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.
Stichworte
Computational Theory and Mathematics; Applied Mathematics; Molecular Biology; Structural Biology
Erscheinungsjahr
2020
Zeitschriftentitel
Algorithms for Molecular Biology
Band
15
Ausgabe
1
Art.-Nr.
4
eISSN
1748-7188
Page URI
https://pub.uni-bielefeld.de/record/2942421

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Wittler R. Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms for Molecular Biology. 2020;15(1): 4.
Wittler, R. (2020). Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms for Molecular Biology, 15(1), 4. doi:10.1186/s13015-020-00164-3
Wittler, R. (2020). Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms for Molecular Biology 15:4.
Wittler, R., 2020. Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms for Molecular Biology, 15(1): 4.
R. Wittler, “Alignment- and reference-free phylogenomics with colored de Bruijn graphs”, Algorithms for Molecular Biology, vol. 15, 2020, : 4.
Wittler, R.: Alignment- and reference-free phylogenomics with colored de Bruijn graphs. Algorithms for Molecular Biology. 15, : 4 (2020).
Wittler, Roland. “Alignment- and reference-free phylogenomics with colored de Bruijn graphs”. Algorithms for Molecular Biology 15.1 (2020): 4.
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2020-04-09T08:57:58Z
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PMID: 32280365
PubMed | Europe PMC

arXiv: 1905.04165

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