Currently, if no phylogenetic tree is uploaded for the selection of query- and reference groups, comma-separated lists of taxon names that are identical to the sequence labels (headers) in the alignment file can be used:
Only upload an alignment and click "Next":

The input page for comma-separated taxon lists appears:

If one of the taxon names in the lists does not exactly match the labels, it is just left out in the analysis without a warning. This means, errors in the labeling can only be recognized by comparing the number of taxon names (sequence labels) from the input with the number of sequences shown next to "Query Group" and "Reference Group" in the results.