Snapshot for sharing

Sharing this release with Chris Brooke's team at the University of Illinois.

This release has a few bug fixes:

• Fixed a bug in convert_reads where stop codons were not being printed.
• Fixed a bug in convert_reads where stop codons were not being considered unambiguous.
• Fixed a bug in calculate_linkage to see that the variant is above the threshold in at least one of the replicates.

And a few enhancements:

• Added columns to tally up unambiguous residues separately from ambiguous residues. This makes the script add_consensus_columns_to_frequency_tables.pl unnecessary.
• Added compute_cutoff.pl script to compute minimum primerID size cutoff.
• Added libexec folder for MAFFT 7.221 to make it portable.
• Added a brief tutorial along with test files.