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CNVphaser is a tool to infer alleles or haplotypes in copy number variable (CNV) genomic regions. The CNVphaser algorithm uses Partition-Ligation–Expectation-Maximization (PL-EM), and users may set three different initial value types. The algorithm can handle missing calls, any number of variant base types, and seed prior copies in the enumeration procedure of the EM algorithm. (For noisy CNV data: MOCSphaser from the same research group).


DNA structural variation; Human genetics


  • Operation: Genetic variation analysis
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.1
  • Maturity: Stable
  • Credit: The National Cancer Institute, the National Institutes of Health (NIH), ARRA.
  • Contact: Michael Q. Zhang mzhang _at_
  • Collection: -


Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ "Inferring haplotypes of copy number variations from high-throughput data with uncertainty." G3 (Bethesda). 2011 Jun;1(1):35-42.
PMID: 22384316
PMCID: PMC3276117

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