RAxML

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Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

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RAxML(Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood-based inference of large phylogenetic trees. It was originally derived from fastDNAml which in turn was derived from Joe Felsenstein’s dnaml, which is part of the PHYLIP package.”

RAxML employs several heuristics to drastically reduce likelihood search times (see Stamatakis et al., 2005 for more details). These heuristics include: 1) building an initial starting tree under parsimony using random stepwise addition; 2) using Lazy Subtree Rearrangements for branch swapping, which saves time for multiple reasons, primarily because branch optimization only occurs for branches adjacent to the insertion point; 3) using GTR + CAT (GTR with per site rate categories) instead of GTR + GAMMA ; and 4) use of simulated annealing, which incorporates a cooling schedule and allows “backward steps” during the hill-climbing process.


The following Modules files should be loaded for this package:

 module load RAxML/RAxML-7.2.6