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Using RAxML-NG in Practice

Abstract : RAxML-NG is a new phylogenetic inference tool that replaces the widely-used RAxML and ExaML tree inference codes. Compared to its predecessors, RAxML-NG offers improvements in accuracy, 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 How to cite: Alexey M. Kozlov and Alexandros Stamatakis (2020).
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Alexey M. Kozlov, Alexandros Stamatakis. Using RAxML-NG in Practice. Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.1.3:1--1.3:25, 2020. ⟨hal-02535311⟩

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