Raxml
From Vd
General Information
RAxML is a very fast serial program for the inference of phylogenies with maximum likelihood method. RAxML offers several different evolutionary models for both DNA and amino acid sequences.
Home Page
http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
Manual
A good overview and help in running RAXML can be found here, under the Manual section. Here you may find the manual, some recommendations and a lot of code examples.