PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
range of options that were designed to facilitate standard phylogenetic
analyses. The main strengths of PhyML lies in the large number of
substitution models coupled to various options to search the space of
phylogenetic tree topologies, going from very fast and efficient methods
to slower but generally more accurate approaches. It also implements two
methods to evaluate branch supports in a sound statistical framework
(the non-parametric bootstrap and the approximate likelihood ratio
test). PhyML was designed to process moderate to large data sets. In
theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to
process a data set is proportional of the product of the number of
sequences by their length. Hence, a large number of sequences can only
be processed provided that they are short. Also, PhyML can handle long
sequences provided that they are not numerous. With most standard
personal computers, the "comfort zone" for PhyML generally lies around 3
to 500 sequences less than 2,000 character long.

WWW: https://github.com/stephaneguindon/phyml/