Li Lab:Softwares

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• Whole Genome Phylogeny

Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis

• 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

Whole-genome shotgun bisulfite sequencing is a powerful tool to detect DNA methylation at single-base resolution. Mapping millions of bisulfite reads remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, multiple CpG heterogeneous methylation within a single read, etc. Hereby, we present the first general-purpose Bisulfite Sequence MAPping program, BSMAP. By combining fast seeding and bitwise masking, BSMAP addresses all the above issues and offers superior performance and flexibility.