Article
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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. https://doi.org/10.20944/preprints201905.0056.v1 Kozlov, A. M.; Stamatakis, A. Using RAxML-NG in Practice. Preprints 2019, 2019050056. https://doi.org/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.)
Keywords
phylogenetic inference; maximum likelihood; parallel processing; HPC
Subject
Computer Science and Mathematics, Computer Science
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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