Suite of programs for the analysis of non-homogeneous substitution processes
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TestNH
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README.md

testnh

Suite of programs for the analysis of non-homogeneous substitution processes

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. The programs depend on the Bio++ libraries. Pre-compiled executables are statically linked (see http://bioweb.me/testnh/releases) and therefore already include all required code from the libraries.

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). Pre-compiled packages will ask for all required dependencies, which can be found in the same download directory. The needed libraries are bpp-core, bpp-seq, bpp-phyl.

For compiling the programs yourself, from the downloaded sources or from the git repository, please follow the instructions from bppsuite.

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 at http://bioweb.me/testnh/releases.

How can I get help?

A dedicated discussion forum is available at Google Groups https://groups.google.com/forum/#!forum/testnh-help-forum.

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.
  • (4) Guéguen L., Duret L., Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Mol Biol Evol. 2017.