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bioRxiv · 10.1101/447110

RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference

Kozlov, A.·Darriba, D.·Flouri, T.·Morel, B.·Stamatakis, A.
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Abstract

MotivationPhylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum like-lihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.\n\nResultsWe 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 to 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 a the recently introduced transfer bootstrap support metric.\n\nAvailabilityThe 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/.\n\nContactalexey.kozlov@h-its.org

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Kozlov, A., Darriba, D., Flouri, T., Morel, B., Stamatakis, A.. 2018-10-18. RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. https://doi.org/10.1101/447110

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