MixHMM specifications


Unique identifier OMICS_02569
Name MixHMM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


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Publication for MixHMM

MixHMM in publications

PMCID: 3957100
PMID: 24672537
DOI: 10.3389/fgene.2014.00051

[…] – the two primary purveyors of snp arrays – offer free software packages for cnv analysis. independently developed toolsets are also available. these include circular binding segmentation () mixhmm (), gada (), penncnv (figure ; ), and parsecnv (; the latter two were developed by emerge researchers and are widely used)., common cnvs are well-covered by snps in existing arrays (; ). […]

PMCID: 3680018
PMID: 23724825
DOI: 10.1186/1471-2164-14-367

[…] tool which is capable of improved detection using parent–child trios, but is not designed to detect upd or partial copy number states []. other hmm-based approaches, including pscn, genocn, mixhmm, and gphmm, can detect cnvs and upd events in tumor/normal mixtures and are thus capable of detecting mosaic changes at a certain level of resolution [-]. a bayesian-based algorithm, gbpcr, […]

PMCID: 3472297
PMID: 22870940
DOI: 10.1186/1471-2105-13-192

[…] methods for cna and loss of heterozygosity (loh) detection on tumour samples were assessed on this synthetic data and on a dilution series of a breast cancer cell-line: ascat, gap, genocna, gphmm, mixhmm and oncosnp. we report the recall rates in terms of normal cell contamination levels and alteration characteristics: length, copy number and loh state, as well as the false discovery rate […]

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MixHMM institution(s)
Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

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