Compare query (observed) vs. reference (expected) sequences.

This action aligns a set of query (e.g., observed) sequences against a set of reference (e.g., expected) sequences to evaluate the quality of alignment. The intended use is to align observed sequences against expected sequences (e.g., from a mock community) to determine the frequency of mismatches between observed sequences and the most similar expected sequences, e.g., as a measure of sequencing/method error. However, any sequences may be provided as input to generate a report on pairwise alignment quality against a set of reference sequences.