For better experience, turn on JavaScript!



m-HMM is a tool to detect copy number variation (CNV) in next-generation sequencing (NGS). The m-HMM algorithm uses a hidden Markov model (HMM) together with emission probabilities that are directed by mixture distributions, and it estimates the parameter values applying the Expectation-Maximization (EM) algorithm.


Genetics; Genetic variation


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2 or v3
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: The National Science Foundation.
  • Contact: Heng Wang hengwang _at_ | Dan Nettleton dnett _at_ | Kai Ying kai.ying _at_
  • Collection: -


Wang H, Nettleton D, Ying K "Copy number variation detection using next generation sequencing read counts." BMC Bioinformatics. 2014 Apr 14;15:109.
PMID: 24731174
PMCID: PMC4021345

Download and documentation

If you find errors, please report here.