RAxML
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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