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

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

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 2.18 MB
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
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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2020-04-09T08:57:58Z
MD5 Prüfsumme
661c8f5e3f179bb0ad5d4338ef914ca9


Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

References

Daten bereitgestellt von Europe PubMed Central.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 32280365
PubMed | Europe PMC

arXiv: 1905.04165

Suchen in

Google Scholar