|  **Note:**  Most software published by our group is also available on [[https://github.com/uci-cbcl | github.com/uci-cbcl]]|



==== Hobbes ====
Hobbes is a tool for very fast, very accurate short-read sequence alignment.  Hobbes has its own [[http://hobbes.ics.uci.edu/ | homepage]].

==== Genomix ====

Parallel genome assembly using Hyracks, available at [[https://github.com/uci-cbcl/genomix|https://github.com/uci-cbcl/genomix]]

==== EXTREME ====
An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data, available at [[https://github.com/uci-cbcl/EXTREME]]

==== PyLOH ====
PyLOH is a tool for discovering copy number variations in cancer genomes. PyLOH is available at 
[[https://github.com/uci-cbcl/PyLOH]]

==== TEMP ====
A tool for transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data, available at [[https://github.com/uci-cbcl/TEMT]]

==== GBMCI ====
GBMCI is a tool for survival analysis by direct concordance index learning using gradient boosting, available at [[https://github.com/uci-cbcl/GBMCI]]
==== AREM ====
AREM is a tool for ChIP-seq analysis, and is able to discover peaks in repeat regions of the genomes. AREM is available at [[software/arem | Aligning Reads from ChIP-seq data by expectation-maximization ]]

==== tree-hmm ====
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]]


==== SGD-RJ ====
[[http://cbcl.ics.uci.edu/sgd | SGD-RJ]] Stochastic gradient descent based on reversible jump MCMC.
==== SSEA ====
[[http://cbcl.ics.uci.edu/SSEA | SSEA]] SNP set enrichment analysis for genome-wide association studies.
==== SiPhy ====
[[http://www.broadinstitute.org/genome_bio/siphy | SiPhy]] site-specific phylogenetic analysis for identifying conserved DNA sequences.

==== DNA-zip ====
[[http://www.ics.uci.edu/~dnazip/index.html | DNAzip]] DNA sequence compression

==== MDOS ====

[[https://github.com/uci-cbcl/mdos|MDOS]] motif discovery using orthologous sequences (alignment independent)

==== iPubMed ====
[[http://ipubmed.ics.uci.edu | iPubMed]]: instant PubMed, featuring interactive and fuzzy search

==== MotifMap ====
[[http://motifmap.ics.uci.edu | 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]].