The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Open accessAbstract
Motivation: Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results: We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation: The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. Supplementary information: Supplementary data are available at Bioinformatics online.
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Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Zhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164
Terraces in phylogenetic tree space
Sanderson, M. J., McMahon, M. M., & Steel, M. (2011) · Science · doi:10.1126/science.1206357 · Cited by 144
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Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
Darriba, D., Posada, D., Kozlov, A. M., Stamatakis, A., Morel, B., & Flouri, T. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz189 · Cited by 2,105
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Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-1926-6 · Cited by 1,327
Self-citationEmergence of genomic diversity and recurrent mutations in SARS-CoV-2
van Dorp, L., Acman, M., Richard, D., Shaw, L. P., Ford, C. E., Ormond, L., Owen, C. J., Pang, J., Tan, C. C. S., Boshier, F. A. T., et al. (2020) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2020.104351 · Cited by 774
Isolation of an archaeon at the prokaryote–eukaryote interface
Imachi, H., Nobu, M. K., Nakahara, N., Morono, Y., Ogawara, M., Takaki, Y., Takano, Y., Uematsu, K., Ikuta, T., Ito, M., et al. (2020) · Nature · doi:10.1038/s41586-019-1916-6 · Cited by 624
Metadata
- Authors
- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-09
- Volume
- 35
- Issue
- 21
- Pages
- 4453-4455
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2949867654
- Cited by
- 4,253
- References
- 4
- FWCI
- 103.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
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