PROmlk is part of the PHYLIP package

Copyright 2000-2004 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 protein amino acid sequences under the constraint that the trees estimated must be consistent with a molecular clock. The molecular clock is the assumption that the tips of the tree are all equidistant, in branch length, from its root. This program is indirectly related to PROml. It uses the Dayhoff probability model of change between amino acids. Its algorithmic details are not yet published, but many of them are similar to DNAMLK.