Li Lab:Softwares

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• HMMTiling

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

• Model-based Analysis of Tiling-array (MAT)

A model-based algorithm for finding enriched regions in ChIP-Chip experiments

• Cis-regulatory Element Annotation System (CEAS)

An integrated webserver for analyzing ChIP-chip data

• extreme MApping of OligoNucleotides (xMAN)

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

• Model-based Analysis of ChIP-sequencing (MACS)

A model-based algorithm for finding enriched regions in ChIP-Seq experiments.

• BSMAP: whole genome Bisulfite Sequence MAPping program

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. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.[math]\displaystyle{ Insert formula here }[/math]