Kozlov, AM;
Darriba, D;
Flouri, T;
Morel, B;
Stamatakis, A;
(2019)
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Bioinformatics
, 35
(21)
pp. 4453-4455.
10.1093/bioinformatics/btz305.
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Abstract
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/.
| Type: | Article |
|---|---|
| Title: | RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/bioinformatics/btz305 |
| Publisher version: | https://doi.org/10.1093/bioinformatics/btz305 |
| Language: | English |
| Additional information: | Copyright © The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10078320 |
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