Table 1.

Commonly (>10 citations) applied CNV detection methods for SNP-array data.

Software	Algorithm	Code	Platform	Year a	Reference	Citations b	Software URL
PennCNV	HMM	Perl	Multiple	2007	[43]	300	http://penncnv.openbioinformatics.org
Birdsuite (Birdseye, Canary)	Mixture models	Java/Python/R	Affymetrix	2008	[44]	300	http://www.broadinstitute.org
Nexus Copy Number	Proprietary (Segmentation)	windows executable	Multiple	-	-	100	http://www.biodiscovery.com
QuantiSNP	HMM	MATLAB	Multiple	2007	[45]	100	http://sites.google.com/site/quantisnp
CNVPartition	Proprietary	windows executable	Illumina	2006	-	100	http://support.illumina.com
Partek Genomics Suite	Proprietary (Segmentation or HMM)	windows executable	Multiple	-	-	30	http://www.partek.com/pgs
CNVFinder	Experimental variability	perl	Array CGH	2006	[46]	30	http://www.sanger.ac.uk/resources/software/cnvfinder/
CGHCall	segmentation and mixture model	R	Array CGH	2007	[47]	30	http://www.few.vu.nl/~mavdwiel/CGHcall.html
GenoCNV	HMM	R	Multiple	2009	[48]	30	http://www.bios.unc.edu/~weisun/software/genoCN.htm
SW-ARRAY	Smith Waterman	R	Array CGH	2005	[49]	30	Not available
HMMSeg	HMM wavelet smoothing	Java	Multiple	2007	[50]	10	http://noble.gs.washington.edu/proj/hmmseg
VanillaICE	HMM	R	Affymetrix	2008	[51]	10	http://cran.r-project.org
CNVHap	HMM, Haplotype	Java	Multiple	2010	[52]	10	http://www.imperial.ac.uk/people/l.coin
dChip	Multiple	R	Multiple	2008	[53]	10	http://sites.google.com/site/dchipsoft
GADA	Bayesian	R	Multiple	2010	[54]	10	http://cran.r-project.org
CNV Workshop	Segmentation	complete VM	Multiple	2010	[55]	10	http://sourceforge.net/projects/cnv

^a Year reference when published. ^b At least this many citations in PubMed or company website at July 2015. Abbreviation: HMM, Hidden Markov Model.