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Protocols

TestNH specifications

Information


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
Requirements
Bio++ libraries
Source code URL http://biopp.univ-montp2.fr/repos/sources/testnh/
Maintained No

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Publication for TestNH

TestNH citations

 (4)
library_books

Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum

2018
Genome Biol Evol
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 of […]

library_books

Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

2017
Mol Biol Evol
PMCID: 5850866
PMID: 29220511
DOI: 10.1093/molbev/msx308

[…] maximum 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. […]

library_books

Hemizygosity Enhances Purifying Selection: Lack of Fast Z Evolution in Two Satyrine Butterflies

2016
Genome Biol Evol
PMCID: 5174731
PMID: 27590089
DOI: 10.1093/gbe/evw214

[…] stop codons ()] and the alignments were cleaned for gaps (by removing all sites that presented a gap in at least one species). We used the programs bppml and mapNH [http://biopp.univ-montp2.fr/forge/testnh (; )] to estimate the synonymous and non-synonymous substitution rate (dS, the number of synonymous substitutions per synonymous site and dN, the number of non-synonymous substitutions per non- […]

call_split

Fast and Robust Characterization of Time Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

2012
PLoS One
PMCID: 3313935
PMID: 22479459
DOI: 10.1371/journal.pone.0033852
call_split See protocol

[…] ation method for counting substitution was implemented from the R code kindly provided by Tataru and Hobolth , and made available to the libraries (version 2.0.2 and later). MapNH is available in the TestNH package at http://biopp.univ-montp2.fr/forge/testnh, as source code and binary versions. The program is written in standard C++ and it compiles in Linux, Windows and MacOS systems, and depends […]


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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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