Consider using Pyrodigal for speeding up the gene prediction

[althonos]

Hi! I saw your tweet and looked into the code of whokaryote, really nice tool.

Since you're using Prodigal, I figured you may be interested in using Pyrodigal (https://github.com/althonos/pyrodigal), which is basically a Python library that wraps Prodigal, so you can install is directly with pip, even on Windows. It's also twice as fast, since I spent some time optimizing the time-critical part of gene scoring, which may peak your interest as well :)

As a side note, you should consider making a release on PyPI, although that would warrant some change in your repository structure.