Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 May 2019 doi:10.20944/preprints201905.0056.v1 Using RAxML-NG in Practice Alexey M. Kozlov1 Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies [Schhloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany]
[email protected] http://orcid.org/0000-0001-7394-2718 Alexandros Stamatakis2 Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Karlsruhe Institute of Technology, Institute for Theoretical Informatics [Schhloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany]
[email protected] https://orcid.org/0000-0003-0353-0691 Abstract RAxML-NG is a new phylogentic inference tool that replaces the widely-used RAxML and ExaML tree inference codes. Compared to its predecessors, RAxML-NG offers improvements in accur- acy, flexibility, speed, scalability, and user-friendliness. In this chapter, we provide practical recommendations for the most common use cases of RAxML-NG: tree inference, branch support estimation via non-parametric bootstrapping, and parameter optimization on a fixed tree topo- logy. We also describe best practices for achieving optimal performance with RAxML-NG, in particular, with respect to parallel tree inferences on computer clusters and supercomputers. As RAxML-NG is continuously updated, the most up-to-date version of the tutorial described in this chapter is available online at: https://cme.h-its.org/exelixis/raxml-ng/tutorial. 2012 ACM Subject Classification Applied computing → Life and medical sciences → Compu- tational biology → Molecular evolution Keywords and phrases phylogenetic inference, maximum likelihood, parallel processing, HPC Supplement Material https://github.com/amkozlov/ng-tutorial Funding This work was financially supported by the Klaus Tschira Foundation 1 Introduction RAxML [21, 22] is a widely-used tool for maximum likelihood (ML) based phylogenetic inference.