pyGEMME is a Python reimplementation of the GEMME package which is lightweight and built in Numpy and Biopython. It is bundled with a notebook for querying the MMSeqs server, using code from the ColabFold package.
The relevant packages can be installed using the Conda package manager by running conda install -n pyGEMME --file environment.yml.
To install the scripts into a virtual environment run pip install -e .
To test the full pyGEMME on the provided MSA (BLAT_ECOLX), run the command python scripts/run_gemme.py -t -p.
To run pyGEMME on a new MSA, run the command python scripts/run_gemme.py -i MSA_FILE -o OUTPUT_DIR -p, replacing MSA_FILE and OUTPUT_DIR with the locations of the desired input MSA file and output directories respectively.
To generate an MSA from the MMSeqs server, a script adapted from the Colabfold package (Martin Steinegger and coworkers) is bundled with pyGEMME. Simply run python scripts/mmseqs_query.py -q UNIPROT_NAME, replacing UNIPROT_NAME with the uniprot name or accession of the target sequence.