TestNH statistics

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TestNH specifications


Unique identifier OMICS_16355
Name TestNH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 1.1.0
Stability No
Bio++ libraries
Source code URL http://biopp.univ-montp2.fr/repos/sources/testnh/
Maintained No



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Publication for TestNH

TestNH in pipeline

PMCID: 5811872
PMID: 29390140
DOI: 10.1093/gbe/evy023

[…] (). apart from the model selection approach, the underlying models of codon sequence evolution are identical to the one originally described by yang (; ). model selection was performed with the testnh software, which contains two programs: 1) mapnh () was used for mapping substitutions on the previously inferred phylogenetic tree and 2) partnh () was subsequently employed to fit time […]

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TestNH in publications

PMCID: 5811872
PMID: 29390140
DOI: 10.1093/gbe/evy023

[…] the authors state that such models should only be used for hypothesis testing and advise against using them for scans of positive selection. proposed a model selection approach (implemented in the testnh package) allowing to select for the best nonhomogeneous model supported by the data. they start by fitting the simplest (homogeneous) model and sequentially add parameters to model variation […]

PMCID: 5850866
PMID: 29220511
DOI: 10.1093/molbev/msx308

[…] likelihood program is called bppml, and is available at the address http://bioweb.me/bppsuite. the stochastic mapping program is called mapnh, and is available at the address http://bioweb.me/testnh., a short tutorial about model inference and stochastic mapping as described in this article is available here: http://bioweb.me/mapdnds., we thank marie sémon for her comments […]

PMCID: 3313935
PMID: 22479459
DOI: 10.1371/journal.pone.0033852

[…] with a low precision (optimization stopped when the improvements in log-likelihood were under 1 log likelihood point). we then used mapnh (software available at http://biopp.univ-montp2.fr/forge/testnh), to obtain dn and ds counts. the results of this analysis are shown in , where the estimated dn/ds of each terminal branch is compared to the body mass of the corresponding leaf. a strong […]

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TestNH funding source(s)
This work was supported by European Research Council grant 232971 (“PopPhyl”) and the French Agence Nationale de la Recherche “Bioinformatique” (ANR-10-BINF-01 “Ancestrome”), and by a postdoctoral fellowship from the Human Frontier Science Program and the CNRS.

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