Software Releases: The computational tools we have developed are available for download and free use by the academic community. 

SCRMshaw (Genome-wide Supervised CRM Prediction)
SCRMshaw is a genome-wide CRM prediction program that learns parameters from a list of CRMs that regulates the same spatial/temporal gene expression pattern, and predicts CRMs with similar functionality genome-wide. The SCRMshaw program is designed for predicting CRMs in the genome sequence of model/non-model species given the known CRMs provided by users. Users can also choose three different scoring schemes to predict CRMs: IMM, PAC and HexMCD.
MET (Motif Enrichment Tool)
This web interface takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif for a dozen model organisms.

METALYSIS and CIS-METALYSIS  (Meta analysis of gene expression data sets)

This Linux-based program is meant for revealing higher level insights from multiple gene expression data sets. In particular, if you have up- and down-regulated gene sets from several different conditions and want to know what might be common to those different gene sets, you can use the Metalysis program. A special version of this program, called "cis-Metalysis" identifies cis-elements (TF binding sites) common to those gene sets.

GEMSTAT (Thermodynamics-based modeling of gene expression from regulatory sequences)
SWAN (Prediction of binding targets of a transcription factor, characterized by a position weight matrix)
This Linux-based program is meant for genome-wide prediction of regulatory targets of a motif using a Hidden Markov Model. It differs from Stubb in that instead of asking Does the sequence have more sites than expected from a random (background) model of sequences?, it asks the question Does the sequence have more sites than the average genome-wide frequency of sites? We have found this new approach to lead to more accurate motif target predictions overall.
EMMA (Prediction and alignment of cis-regulatory modules)
This Linux-based program is meant for prediction of regulatory targets of a motif using two-species comparison. If you have a sequence window of length ~100 bp - 2000 bp, and its orthologous window from another species, use EMMA to score the window for matches to a given motif. EMMA is also useful for alignment of cis-regulatory modules (enhancers) between two species, if you have knowledge of the relevant transcription factor motifs.
GenomeSurveyor (Prediction of motif targets in D. melanogaster)
This web-based Genome Browser allows you to find regulatory targets of a large collection of transcription factors in the Drosophila genome. You may use cross-species comparison among 12 genomes to see conserved targets.
CRM discovery benchmark (Data sets from D. melanogaster.) 
Morph software (Probabilistic alignment of cis-regulatory modules) 
D2Z software (Alignment free comparison of regulatory sequences.) 
Indelign software (Probabilistically annotating indels in multiple alignments) 
DIPS software (For finding discriminative PWM motifs) 
Stubb software (For finding cis-regulatory modules) 
PhyME software (Motif finding in orthologous sequences) 
YMF software YMF Web Server (Motif finding)