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MotifMap: A comprehensive map of regulatory motif sites in human and model organisms.

An older version of MotifMap, as published in our first paper and specific to the human dataset is available at http://www.ics.uci.edu/~xhx/project/MotifMap.

Hobbes is a tool for very fast, very accurate short-read sequence alignment. Hobbes has its own homepage.

TEMP is a tool for transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data, and is available at https://github.com/uci-cbcl/TEMT

Tree-HMM is an extension of the popular ChromHMM for doing clustering of epigenetic markers. Given a complete set of epigenetic markers for several cell types, and the phylogeny describing their relationship, Tree-HMM will perform approximate inference on the graphical model induced by connecting genomic positions of a certain cell type in a chain while also connecting different species according to the tree. Thus, each internal node's state depends on its “vertical parent” (parent cell type) and its “horizontal parent” (adjacent genomic region).

Code is available at https://github.com/uci-cbcl/tree-hmm and some sample data is available at http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data

AREM is a tool for ChIP-seq analysis, and is designed to be able to discover peaks in repeat regions of the genomes. The software is available at Aligning Reads from ChIP-seq data by expectation-maximization

SGD-RJ Stochastic gradient descent based on reversible jump MCMC.

SSEA SNP set enrichment analysis for genome-wide association studies.

SiPhy site-specific phylogenetic analysis for identifying conserved DNA sequences.

DNAzip DNA sequence compression

MDOS motif discovery using orthologous sequences (alignment independent)