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TestNH is currently in version 1.1.0. It is based on Bio++ 2.2.0 and is available through the Bio++ forge along with the libraries at http://biopp.univ-montp2.fr/repos/.

What does TestNH do?

TestNH is a package dedicated to the testing of non-homogeneous process in sequence evolution.

What does it provide?

It currently contains the following programs:

  • testnh implements the Bowker test for sequence non-stationarity, as described in (3)
  • mapnh performs substitution mapping and cluster branches according to their underlying substitution processes, as described in (1) and (2)
  • partnh fits a non-homogeneous model of evolution according to branch partitions, as defined from a clustering tree. It can test different sets of partitions and use a model selection criterion to select the appropriate number of clusters as described in (2)
  • randnh generates random non-homogeneous models using two models of non-homogeneity, corresponding to the clustering algorithms implemented in mapnh.

How can i get it?

The TestNH programs are command-line driven. You can get executable files pre-compiled for your system (if there are any), use pre-compiled packages (if there are any) or compile the programs yourself (should work on any system with a decent C++ compiler).

The programs depend on the Bio++ libraries. Pre-compiled executables are statically linked, and therefore already include all required code from the libraries. Pre-compiled packages will ask for all required dependencies, which can be found in the same download directory. For compiling the programs yourself, from the downloaded sources or from the git repository, please follow the instructions from the Bio++ website http://biopp.univ-montp2.fr/wiki/index.php/Installation.

How do I use it?

Several example data sets are distributed along with the source code of the package. A reference manual is also available here, or can be downloaded as PDF.

How can I get help?

A dedicated discussion forum is available at Google Groups

References

(1) Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B. Efficient selection of branch-specific models of sequence evolution. Mol Biol Evol. 2012 Jul;29(7):1861-74.
(2) Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V. Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS One. 2012;7(3):e33852.
(3) Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol. 2008 Sep 22;8:255.

Last modified 3 years ago Last modified on Oct 22, 2014, 12:40:42 PM