UNIT 6.14 Using RAxML to Infer Phylogenies

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. © 2015 by John Wiley & Sons, Inc.