For better experience, turn on JavaScript!



hsegHMM is a software tool to analyze copy number variation (CNV). The hsegHMM algorithm uses a hidden Markov model (HMM) as the basis that includes hypersegmentation and an E-M method.


Genetics; DNA structural variation; Oncology


  • Operation: Polymorphism detection; Sequence analysis; Structural variation detection
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 0.0.4
  • Maturity: Stable
  • Credit: The Intramural Research Program of US National Institutes of Health, National Cancer Institute.
  • Contact: Hyoyoung Choo-Wosoba hyoyoung.choo-wosoba _at_
  • Collection: -


Choo-Wosoba H, Albert PS, Zhu B "hsegHMM: hidden Markov model-based allele-specific copy number alteration analysis accounting for hypersegmentation." BMC Bioinformatics. 2018 Nov 14;19(1):424.
PMID: 30428830
PMCID: PMC6236906

Download and documentation

If you find errors, please report here.