RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics

Abstract

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, phylogenetic difficulty prediction, genotype evolution models, to name but the most important ones. Furthermore, we introduce two novel search heuristics at production code level: the adaptive difficulty-aware heuristic (default) and the fast mode with early-stopping that prevents over-optimization. We perform extensive benchmarking of RAxML-NG 2.0 with respect to its accuracy and speed, and compare it to other popular maximum likelihood based phylogenetic inference tools (IQTree, VeryFastTree) as well as to preceding RAxML-NG versions. In particular, the new fast search heuristic in conjunction with machine learning based branch support prediction induces a 75x inference time reduction compared to RAxML-NG 1.2, with minor to no accuracy loss. The code is available under GNU GPL at https://codeberg.org/amkozlov/raxml-ng.