This page allows the identification of mutations in AB1 and get the corresponding amino acid mutation for both homogeneous and heterogeneous sites.
Whereas anything called differently or as a degenerate base in the AB1 automatic calling is interpreted, secondary peaks are only considered if they are above a given background noise threshold.
The noise is calculated from the average variation in secondary peaks. This is generally fairly unless there is a strong contaminant or there is a frameshift in part of the pool, which would be visible as a sudden increase in noise in the noise plot.
The app does not do a sophisticated alignments as there is no need —there should be one or two mutations different.
If you get garbage out, you may have a contaminant, in which case your best bet is to blast it to find out where it came from.
Links to academic resources and academic social media presence of the authors