EMnEM is a DNA motif finder that takes multiple alignments and a
phylogenetic tree and identifies conserved patterns.
Like modern phylogenetics methods and many motif finding methods it
uses probabilistic models of DNA sequences and their evolution.
The key idea introduced in EMnEM was to use a different model of
evolution, m, for the
motifs and for the background sequence, and to equate the probabilities
in the motif matrix, f, to
the prior probabilities of observing the ancestral bases in the motif
evolution model, p(A|m).
It was described in this paper:
Moses AM, Chiang
DY, Eisen MB: Phylogenetic Motif Detection by Expectation Maximization
on Evolutionary Mixtures.
Pacific Symposium on Biocomputing 2004,9:324-335
the software, source code and instructions.