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

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

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.

The TestNH programs are command-line driven. The programs depend on the Bio++ libraries.

For compiling the programs yourself, from the downloaded sources or from the git repository, please follow the instructions from bppsuite and up to date mapnh.

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.

• (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.