Li:Softwares

A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays
 * HMMTiling

A model-based algorithm for finding enriched regions in ChIP-Chip experiments
 * Model-based Analysis of Tiling-array (MAT)

An integrated webserver for analyzing ChIP-chip data
 * Cis-regulatory Element Annotation System (CEAS)

A intuitive and efficient algorithm for the mapping of millions of query oligonucleotide fragments to the genome of any given length, at least an order of magnitude faster than other popular existing tools
 * extreme MApping of OligoNucleotides (xMAN)

A model-based algorithm for finding enriched regions in ChIP-Seq experiments.
 * Model-based Analysis of ChIP-sequencing (MACS)

BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage.
 * BSMAP: whole genome Bisulfite Sequence MAPping program