Table 5.

Software tools for epigenomics data processing and analyses

	Software Tools	Methylation Analysis
1.	Batman	http://td-blade.gurdon.cam.ac.uk/software/batman
2.	BDPC	http://biochem.jacobs-university.de/BDPC
3.	Epinexus	http://epinexus.net/home.html
4.	MethDB	http://www.methdb.de
5.	methPrimerDB	http://medgen.ugent.be/methprimerdb
6.	MethyCancer Database	http://methycancer.psych.ac.cn
7.	Methylumi	http://www.bioconductor.org/packages/bioc/html/methylumi.html
8.	mPod	http://www.compbio.group.cam.ac.uk/Projects/p4meth.html
9.	PubMeth	http://www.pubmeth.org
10.	QUMA	http://quma.cdb.riken.jp
11.	TCGA Data Portal	http://cancergenome.nih.gov/dataportal
	Software Tools	Bisulphite Sequencing Analysis
1.	BSMAP	http://code.google.com/p/bsmap
2.	MethBLAST	http://medgen.ugent.be/methBLAST
3.	methPrimer	http://www.urogene.org/methprimer
4.	Methyl Primer Express	http://www.appliedbiosystems.com/methylprimerexpress
5.	CpGviewer	http://dna.leeds.ac.uk/cpgviewer
	Software Tools	CpG Island Analysis
1.	CpGcluster	http://bioinfo2.ugr.es/CpGcluster
2.	CpGFinder	http://linux1.softberry.com
3.	CpG Island Explorer	http://bioinfo.hku.hk/cpgieintro.html
4.	CpG Island Explorer	http://cpgislands.usc.edu
5.	CpG Promoter	http://www.cshl.edu/OTT/html/cpg_promoter.html
6.	CpG ratio/GC content Plotter	http://mwsross.bms.ed.ac.uk/public/cgi-bin/cpg.pl
7.	EMBOSS CpGPlot/CpGReport/Isochore	http://www.ebi.ac.uk/Tools/emboss/cpgplot/index.html