GitHub - BioPP/testnh: Suite of programs for the analysis of non-homogeneous substitution processes (original) (raw)

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.

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

Otherwise, those programs are available in a singularity image there.

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 atpbil.

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.