We offer a Docker image with GEMME and all its dependencies installed. First, you need to install Docker from the Docker website. Then, to run the image:

docker run -ti --rm --mount type=bind,source=$PWD,target=/project elodielaine/gemme:gemme

Then, if you have an alignment file in FASTA format in your directory, let's say aliBLAT.fasta, you can try and run GEMME like this:

python2.7 $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta

In case your input alignment file is in A3M format, for instance aliBLAT.a3m, please convert it to FASTA format prior to running GEMME:

convertAli.sh aliBLAT

Alternatively, you may download the package and install it. The dependencies are:

- Joint Evolutionary Trees

- seqinr R package

To install the tool, please do the following:

1- Download the GEMME.tgz archive here.

2- Uncompress the archive in the directory of your choice.

3- Define and export the environment variable GEMME_PATH=/path-to-GEMME-directory/.

4- Run the program by typing "python $GEMME_PATH/gemme.py inputAli.fasta".

5- A help can be accessed by typing "python $GEMME_PATH/gemme.py --help".