fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. Much of this program is based o�n version 3.3 of Joseph Felsenstein's DNAML program (this is to give him credit, not to have you contact him for information o�n fastDNAml). This program implements the maximum likelihood method for DNA sequences. The present version is faster than earlier versions of DNAML. Details of the algorithm are published in the paper by Felsenstein and Churchill (1996). The model of base substitution allows the expected frequencies of the four bases to be unequal, allows the expected frequencies of transitions and transversions to be unequal, and has several ways of allowing different rates of evolution at different sites.

References:
Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48 [Entrez]

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.