. Author manuscript; available in PMC: 2009 Sep 21.

Published in final edited form as: Int J Comput Biol Drug Des. 2008 Jan 1;1(4):368–395. doi: 10.1504/IJCBDD.2008.022208

Table 2.

Selected software for use in copy number data analysis

	Normalisation	Smoothing	Calling CNVs	Web address
aCGH		X	X	http://bioconductor.org/
CGHPRO	X	X		http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/
ITALICS	X	X	X	http://bioconductor.org/
MANOR	X			http://bioconductor.org/
Rob-HMM (in CNA-HMMer software)	X		X	http://www.cs.ubc.ca/~sshah/acgh/
snapCGH	X	X	X	http://bioconductor.org/
dChip	X		X	http://biosun1.harvard.edu/complab/dchip/
CNAT	X	X	X	http://www.affymetrix.com/support/technical/software_downloads.affx
CRLMM (in the oligo package)	X	X	X	http://bioconductor.org/
CGH-Explorer		X		http://www.softgenetics.com/CGHExplorer.html
CGH-Minor			X	http://www-stat.stanford.edu/~wp57/CGH-Miner/
GLAD		X		http://bioconductor.org/
DNAcopy			X	http://bioconductor.org/
SMAP			X	http://bioconductor.org/
QuantiSNP			X	http://www.well.ox.ac.uk/QuantiSNP/
VanillaICE			X	http://bioconductor.org/
PennCNV			X	http://www.neurogenome.org/cnv/penncnv/
Illumina BeadStudio			X	http://www.illumina.com/pages.ilmn?ID=169
Birdsuite	X	X	X	http://www.broad.mit.edu/mpg/birdsuite/
CNAM	X		X	http://www.goldenhelix.com/SNP_Variation/CNAM/index.html