Software

• Nucleosome Positioning from Sequencing (NPS)
  A signal processing-based algorithm for identifying positioned nucleosomes fromsequencing experiments at the nucleosome level
• Model-based Analysis of ChIP-Seq (MACS)
  A model-based algorithm for finding enriched regions in ChIP-Seq experiments
• extreme MApping of OligoNucleotides (xMAN)
  A simple and efficient method for the mapping of millions of queryoligonucleotide fragments to the subject genome of any given length, at leastan order of magnitude faster than other popular existing tools
• Model-based Analysis of 2-Color Arrays (MA2C)
  A model-based algorithm for analyzing 2-color microarrays. 
• Microarray Blob Remover (MBR)
  A microarray JAVA tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step
• Cis-regulatory Element Annotation System(CEAS) - Standalone version
  A standalone Python package for analyzing ChIP-chip/seq data
• Cis-regulatory Element Annotation System(CEAS)
  An integrated webserver for analyzing ChIP-chip data
• Model-based Analysis of Tiling-array (MAT)
  A model-based algorithm for finding enriched regions in ChIP-Chip experiments
• CompareProspector
  A sequence motif-finding algorithm 
• Motif Regressor
  A program for finding DNA sequence motifs 
• MDscan
  A Fast and Accurate Motif Finding Algorithm With Applications To Chromatin Immunoprecipitation Microarray Experiments 
• BioProspector
  Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-ExpressedGenes 

Last modified by HB Sept 25, 2009