Using RAxML to Infer Phylogenies

Current Protocols in Bioinformatics
Alexandros Stamatakis

Abstract

Inference of phylogenetic trees under the maximum likelihood (ML) criterion represents a routine task in biological data analysis. In this unit we describe how to plan analyses and use Randomized Accelerated Maximum Likelihood (RAxML) for phylogenetic inferences under ML, how to infer support values using the standard bootstrap procedure as well as other statistical measures, and how to conduct post-analyses on collections/sets of phylogenetic trees including statistical significance tests and consensus tree methods. We also discuss what measures can be taken and what further analyses can be conducted when relationships in the inferred tree exhibit "low" support.

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Citations

Nov 28, 2017·Molecular Biology and Evolution·Xiaofan ZhouAntonis Rokas
Apr 17, 2018·Genome Biology and Evolution·Anna M FlorianoDavide Sassera
Sep 26, 2017·International Journal of Systematic and Evolutionary Microbiology·Laura B GoodmanJasna Kovac
Nov 4, 2017·Environmental Microbiology·Craig W HerboldCécile Gubry-Rangin
Oct 24, 2019·MSystems·Lin-Xing ChenJillian F Banfield
Apr 13, 2018·BMC Evolutionary Biology·A D LokitsP F Stadler
Mar 12, 2016·PloS One·Martin HoeniglSanjay R Mehta
Oct 20, 2017·Emerging Infectious Diseases·Hasan EjazEva Heinz
Jul 6, 2019·Frontiers in Microbiology·Dmitry A RodionovAndrei L Osterman
Aug 31, 2020·Journal of Molecular Evolution·Thu Le Kim, Vinh Le Sy
Sep 11, 2020·Nature Communications·Alaina R Weinheimer, Frank O Aylward
Jul 12, 2018·Scientific Reports·Ericka KirkpatrickFlorian Krammer
May 7, 2019·Frontiers in Microbiology·Abakabir Mahamat AbdelrahimOlivier Firmesse
Feb 16, 2020·Molecular Biology and Evolution·Antonio BrunEnrique Caviedes-Vidal
Feb 20, 2020·Scientific Reports·Ana LokmerLaure Ségurel
Feb 12, 2020·Science Advances·Jonathan H BethkeLingchong You
Jun 8, 2018·Molecular Biology and Evolution·Claudia Augusta de Moraes Russo, Alexandre Pedro Selvatti

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