RAxML (Randomized Axelerated Maximum Likelihood) is a free and open source, command line based tool for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.

RAxML has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
   
In addition to the sequential version, RAxML offers two ways to exploit parallelism: fine-grained parallelism that can be exploited on shared memory machines or multi-core architectures and coarse-grained paral- lelism that can be exploited on Linux clusters.
   
The current version of RAxML is a highly optimized program, which handles binary, DNA, RNA secondary structure, multi-state morphological, and AA alignments under various models of substitution and several distinct methods of rate heterogeneity.

How to install and run: Unarchive, open a Terminal window, go to the RAxML's folder and run the following commands from the command line:

make -f Makefile.gcc
./raxmlHPC

To have RAxML run about 30-50% faster:

make -f Makefile.SSE.gcc
./raxmlHPC-SSE3

One may also compile a Pthreads version with and without SSE3 intrinsics:

make -f Makefile.PTHREADS.gcc
./raxmlHPC-PTHREADS

and for a 30-50% performance boost:

make -f Makefile.SSE3.PTHREADS.gcc
./raxmlHPC-PTHREADS