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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Einrichtung
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
Urheberrecht / Lizenzen
eISSN
1748-7188
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2942421
Zitieren
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, Roland. 2020. “Alignment- and reference-free phylogenomics with colored de Bruijn graphs”. Algorithms for Molecular Biology 15 (1): 4.
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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Daten bereitgestellt von European Bioinformatics Institute (EBI)
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Daten bereitgestellt von Europe PubMed Central.
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PMID: 32280365
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arXiv: 1905.04165
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