dnaml is part of the PHYLIP package

Copyright 1986-2004 by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

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:
Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.