Fixed args in call to `toStr` in `proteins-to-pathogens-civ.py`.
3.1.1
Not secure
Added `dark.civ` to packages in `setup.py`.
3.1.0
Not secure
Added `make-protein-database.py`, `download-genbank.sh`, and `parse-genbank-flat-file.py` scripts, as well as `doc/protein-database.md` with some instructions on how to make a protein database. Added CIV (Charite Institute of Virology) scripts `proteins-to-pathogens-civ.py` and `alignment-panel-civ.py`.
3.0.80
Not secure
Added `bin/create-newick-relabeling-output.py` and `bin/relabel-newick-tree.py`.
3.0.79
Not secure
Add `--omitVirusLinks` and `--omitSampleProteinCount` options to `proteins-to-pathogens.py` to make HTML output less confusing when running on RVDB or OKIAV databases. Removed highlighting of pathogens with high protein fraction since that was done in a non-useful way. Removed index field from HTML output and removed HSP count unless it differs from the read count.