MACS : Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa).
Peakseq : program for identifying and ranking peak regions in ChIP-Seq experiments.
S-Mart : An intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.
SICER : Package for identification of enriched domains from histone modification ChIP-Seq data.
MEME-ChIP : Tool designed especially for discovering motifs in LARGE (50MB maximum) sets of short (around 500bp) DNA sequences centered on locations of interest such as those produced by ChIP-seq experiments.
GEM : A Java software for studying protein-DNA interaction using ChIP-seq/ChIP-exo data.
DREME : A tool for motif discovery in transcription factor ChIP-seq data .
Bis-SNP : Bisulfite Space genotyper and Methylation caller.
Bsmap : A short reads mapping software for bisulfite sequencing reads.
BRAT : An accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.
BatMeth : Improved mapper for bisulfite sequencing reads on DNA methylation.
B-SOLANA : A fast and accurate all-in-one approach including alignment and methylation calling of two-base encoding (colorspace) bisulfite sequencing data.
PASS-bis : A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Bismark : A tool to map bisulfite converted sequence reads and determine cytosine methylation states.
Kismeth : An online tool for analysis of bisulphite treated reads.
BS Seeker : Performs accurate and fast mapping of bisulfite-treated short reads .
NGSmethPipe : A tool to generate high-quality methylation maps.
BSmooth-align : A tool for alignment of bisulfite sequence reads and tabulation of read-level methylation measurements.
Methylkit : An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
Methylumi : This package provides classes for holding and manipulating Illumina methylation data.
MethylCoder : Performs methylation analysis in single base pair resolution.