RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics
RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, we describe the next major release, RAxML-NG 2.0. It introduces a plethora of new features: integrated model testing, multiple fast branch support metrics, automatic parallelization tuning,…
RAxML-NG 2.0, the latest version of the widely-used maximum likelihood based phylogenetic inference tool, has been released after seven years of continuous improvement. This new release boasts a multitude of new features, including integrated model testing, multiple fast branch support metrics, automatic parallelization tuning, phylogenetic difficulty prediction, and genotype evolution models.
Two novel search heuristics have also been introduced at the production code level: the adaptive difficulty-aware heuristic, which is now the default, and a fast mode that incorporates early-stopping to prevent over-optimization.
RAxML-NG 2.0's performance has been extensively benchmarked, demonstrating a remarkable 75-fold reduction in inference time when compared to its predecessor, RAxML-NG 1.2, while maintaining accuracy or even showing minor to no loss. The fast search heuristic, when paired with machine learning-based branch support prediction, significantly enhances the tool's efficiency. All of RAxML-NG 2.0's code is available under the GNU GPL license for download at https://codeberg.org/amkozlov/raxml-ng.
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