Using RAxML to Infer Phylogenies.
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.
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.|Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
Alexandros
A
Stamatakis
D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D005828:Genetics, Population; D016013:Likelihood Functions; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny
bootstrap support; consensus tree methods; maximum likelihood; phylogenetics