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.

• DyChIPS: An integrate solution fo dynamic analysis of ChIP-sequencing

DyChIPS is designed for comparative analysis of ChIPSeq data such as protein binding or histone modification. By adjust the minimal peak width and minimal distance between neighboring peaks, DyChIPS can be easily used on protein binding data (alway sharp peaks) or histone modification data (always broad peaks)

• DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS is specifically developed for comparison between nucleosome maps generated based on high-throughput sequencing, it detects changes in nucleosome position, enrichment, or fuzziness at single nucleotide resolution.