Preprint Article Version 1 This version is not peer-reviewed

Using RAxML-NG in Practice

Version 1 : Received: 3 May 2019 / Approved: 6 May 2019 / Online: 6 May 2019 (11:12:20 CEST)

How to cite: Kozlov, A.M.; Stamatakis, A. Using RAxML-NG in Practice. Preprints 2019, 2019050056 (doi: 10.20944/preprints201905.0056.v1). Kozlov, A.M.; Stamatakis, A. Using RAxML-NG in Practice. Preprints 2019, 2019050056 (doi: 10.20944/preprints201905.0056.v1).

Abstract

RAxML-NG is a new phylogentic inference tool that replaces the widely-used RAxML and ExaMLtree inference codes. Compared to its predecessors, RAxML-NG offers improvements in accur-acy, flexibility, speed, scalability, and user-friendliness. In this chapter, we provide practicalrecommendations for the most common use cases of RAxML-NG: tree inference, branch supportestimation 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, inparticular, with respect to parallel tree inferences on computer clusters and supercomputers. AsRAxML-NG is continuously updated, the most up-to-date version of the tutorial described inthis chapter is available online at: https://cme.h-its.org/exelixis/raxml-ng/tutorial .

Supplementary and Associated Material

https://cme.h-its.org/exelixis/raxml-ng/tutorial: On-line version of this tutorial
https://github.com/amkozlov/ng-tutorial: Data files (alignments etc.)

Subject Areas

phylogenetic inference; maximum likelihood; parallel processing; HPC

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