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

By Alexey M. Kozlov, Diego Darriba, Tomás Flouri, Benoit Morel, Alexandros Stamatakis. bioRxiv, 2018

3,694 citations recorded by the source corpus.

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 like-lihood (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. It compares favorably to IQ-Tree, an increasingly popular recent tool for ML-based phylogenetic inference. 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. Availability 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/. Contact alexey.kozlov@h-its.org

View Paper: https://www.semanticscholar.org/paper/26640f9d57cf1e757ae27d093d6b087a7d838f07

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Citations in the corpus

Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “1.3) 95 and RAxML-NG, and enabling higher levels of parallelization for a given tree search.”
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 (2020, methodology): “Subsequently a maximum likelihood phylogenetic tree was built using the Augur tree implementation selecting RAxML as the tree-building method (Kozlov et al., 2019).”
IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, unknown): “Partitioned models are available in RAxML (Stamatakis 2014), RAxML-NG (Kozlov et al. 2019), and IQ-TREE 2 (Minh et al. 2020b); and tools like PartitionFinder (Lanfear et al. 2017) can merge partitions to reduce over-parameterization.”
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2019, methodology): “2008) and RAxML-NG software (Kozlov et al. 2019), by allowing for user-defined mixture models using the “MIXfmodel1,.”
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML (2020, methodology): “For guidelines of which RAxML version to use for particular objectives and datasets, please refer to (Kozlov et al., 2019).”
Using PhyloSuite for molecular phylogeny and tree‐based analyses (2023, methodology): “For example, for sequence alignment, there are MAFFT [4], MUSCLE [5], PRANK [6], and etc.; for phylogenetic tree reconstruction, commonly used programs are IQ ‐ TREE [7], RAxML [8, 9], MrBayes [10], etc. Finally, these programs often use very different input and output file formats.”