Added code to combine multiple sequences (see `bin/combine-sequences.py`).
3.1.76
Not secure
Changed `--maskNoCoverage` to `--maskLowCoverage` in `make-consensus.py` and have it take an argument of the minimum coverage at which to call the consensus.
3.1.75
Not secure
Added `--sample-ploidy 1` to halpotype calling in `bowtie2.py`.
3.1.74
Not secure
Improved `aa-info.py` to also match on partial full names. Improved taxonomic detection of plant-only viruses.
3.1.73
Not secure
Added `count` variable to `format-fasta.py` and a `--start` option to set its starting value.
3.1.72
Not secure
Added `format-fasta.py` script. Reverted unecessary hacks to `fasta-sequences.py` to print MD5 sums, etc.