Cluster diversity and isolation indices

The only efficient way to do these comparisons is using some SQL and scripting. You'll need the Phamerator database underlying these calculations, which is available from http://databases.hatfull.org/Actino_Draft/. It's the "Actino_Draft.sql" file. You'll also need an SQL client on your computer to enable the running of queries on that database. The database is a MySQL database, so this should be the place to start: https://www.mysql.com/downloads/. We scripted in python, using a connector to access the database: https://dev.mysql.com/doc/connector-python/en/connector-python-example-connecting.html. Bio-python is also valuable for these calculations: https://biopython.org/. 

The formulas for the actual calculations are in the paper, so from there it's a matter of querying the database for the phams of interest, and doing the math to compare them. Since these sorts of scripts are heavily computer- and environment-dependent, it doesn't really make sense for us to share ours, unfortunately.

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