Article
Version 1
Preserved in Portico This version is not peer-reviewed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. 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.
Comments (0)
We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.
Leave a public commentSend a private comment to the author(s)
* All users must log in before leaving a comment
