Dark-matter

Added `bin/create-newick-relabeling-output.py` and `bin/relabel-newick-tree.py`.

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.

Fixed silly import error.

Added link to per-pathogen reads in protein-to-pathogens HTML output for
Julia.

Slightly adjust appearance of HTML links for pathogens.

Added search link for ICTV for viruses in HTML output.