INTAA-conservation implements the evolutionary conservation calculations featured in the Amino Acid Interactions (INTAA) web server; however, it can also be used as a stand-alone tool.
Extract the archive, then install the Python dependencies: python3 -m pip install -r requirements.txt. The script database/download_Swiss-Prot.sh can be used to download an example sequence database.
The HMMER software package, including the Easel tools, must be installed and the programs available in the $PATH. All development and testing is done using HMMER 3.3.
Use
code/INTAA-conservation.py PDB_file sequence_database
to calculate the information content for the amino acid residues in the PDB_file using the sequence_database to construct the multiple sequence alignments.