PHYML
PHYML is a software method for building phylogenies from DNA and protein sequences using maximum likelihood. Data sets can be analyzed under several models of evolution (JC69, K80, F81, F84, HKY85, TN93 and GTR for nucleotides and Dayhoff, JTT, mtREV, WAG, DCMut, RtREV, CpREV, VT, Blosum62 and MtMam for amino acids). A discrete-gamma model (Yang, 1994) is implemented to accommodate rate variation among sites. Invariable sites can also be taken into account. PHYML has been extensivle compared to several other software packages by its authors. The results indicate that its topological accuracy is at least as high as that of fastDNAml, while being much faster.
If you use PHYML, please cite: Guindon S, Gascuel O. (2003) "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Syst Biol 52(5):696-704.
Manual: http://atgc.lirmm.fr/phyml/usersguide_cmdline.html
INPUT = Aligned Protein or DNA Sequences (Character Matrix)
TEST INPUT FILES
Input file: phyml_input1.txt
TEST OUTPUT FILES
Output file (tree): phyml_output_trees.txt
Output file (stat): phyml_output_stats.txt