StxTyper version 1.0.45 no longer counts aligning stop codons in the amino-acid percent identity calculation. Including it was an oversight initially. We include the stop codon internally for alignment purposes because it help BLAST extend alignments with mismatches at the last amino-acid.

This change will make a slight change in the percent identities and coordinates of most hits. We have run this on >200,000 E. coli genomes and it never changed the type call, so the effect of this change should be minimal.