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polyHap is a tool to phase and estimate missing genotypes in copy number variable (CNV) regions. The polyHap algorithm uses a hidden Markov model (HMM).


Population genetics


  • Operation: Phasing; Imputation
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X
  • License: Other
  • Cost: Free for non-commercial use
  • Version name: v2
  • Maturity: Stable
  • Credit: -
  • Contact: Shu-Yi Su _at_ | Jonathan White jon.white _at_ | David J Balding d.balding _at_ | Lachlan JM Coin l.coin _at_
  • Collection: -


Su SY, White J, Balding DJ, Coin LJ "Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions." BMC Bioinformatics. 2008 Dec 1;9:513.
PMID: 19046436
PMCID: PMC2647950

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