Tutorial

Installing GeneRax

Open a terminal and install GeneRax:

git clone --recursive  https://github.com/BenoitMorel/GeneRax.git
cd GeneRax
./install.sh

You should obtain a generax executable under build/bin. Then add GeneRax to your path: either copy the executable to a directory that is already in your path or append the absolute path to build/bin to your path. For instance, I had to add the following line to my ~/.bashrc file and to reopen a terminal:

# WARNING!! You need to edit the following path
export PATH="$PATH:/home/benoit/github/GeneRax/build/bin"

Check that GeneRax was correctly installed:

generax --help

This should display a short help message. To get more help, check the wikiwiki.

Reconciliation with GeneRax (without gene tree correction)

We will now reconcile two gene trees with a species tree. We will us gene trees that were inferred from gene MSAs with RAxML-NG. From the root of the GeneRax repository, type:

generax --families examples/gene_tree_correction/ --species-tree data/plants/species_trees/speciesTree.newick --rec-model UnrootedDL --prefix no_correction --strategy EVAL

The file families_plants.txt contains information about the gene families (the gene trees, the gene-species mappings, and the substitution model to use).