RAxML

RAxML (Randomized Axelerated Maximum Likelihood) is a program for maximum likelihood phylogeny estimation for interpreting relationships between sets of data.

Documentation

• RAxML home
• Citation: A. Stamatakis: “RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. In Bioinformatics, 2014, open access.

Usage on Bridges-2

To see what versions of RAxML are available and if there is more than one, which is the default, along with some help, type

module spider raxml

To use RAxML, include a command like this in your batch script or interactive session to load the RAxML module: (note ‘module load’ is case-sensitive):

module load RAxML

Usage on Bridges

To see what versions of RAxML are available type

module avail raxml

To see what other modules are needed, what commands are available and how to get additional help type

module help raxml

To use RAxML, include a command like this in your batch script or interactive session to load the RAxML module:

module load raxml

Be sure you also load any other modules needed, as listed by the module help raxml command.