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.
3.0.78
Not secure
Fixed silly import error.
3.0.77
Not secure
Added link to per-pathogen reads in protein-to-pathogens HTML output for Julia.