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

Please cite as:
P. Ray, S. Shringarpure, M. Kolar and E. P. Xing, CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing, PLoS Computational Biology (2008), Vol 4 (6), June 2008
PDF to be found here.