CSMET is a multispecies supervised motif finder. It uses phylogenetic shadowing
techniques, using mixtures of trees to model every site in the alignment. It also
has an explicit phylogenetic model of functional turnover in motifs. Sites in the input alignment
are autocorrelated by a simple HMM.

CSMET was developed at the SAILING lab in the School of Computer Science, Carnegie
Mellon University, Pittsburgh PA, USA