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PSE-HMM is a tool to detect copy number variation (CNV) in next-generation sequencing (NGS) data with mate-pairs. The PSE-HMM algorithm uses position-specific, a Gaussian mixture distribution, to model CNVs.


Genetics; Genetic variation


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: Matlab
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1
  • Credit: Iran National Science Foundation.
  • Contact: Seyed Amir Malekpour a.malekpour _at_
  • Collection: -


Malekpour SA, Pezeshk H, Sadeghi M "PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities." BMC Bioinformatics. 2016 Nov 3;18(1):30.
PMID: 27809781
PMCID: PMC5445519

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