Hi, I have recently started using the Unipept tool application on your Galaxy platform. I noticed a good level of peptide taxonomic annotation, often reaching genus or species levels. As a test, I made a check on a selection of 2000 peptides using also the Unipept web application (http://unipept.ugent.be/) in order to compare the results of the two applications. Strangely, I observed dramatic differences concerning mainly the depth of taxonomic level annotation; it seems that Unipept on Galaxy doesn’t give sufficient consideration to LCA (as an example 25% of peptides that were classified as root or at superkingdom level using the web application were classified at genera or species level using Galaxy). I think that this could be a problem. In addition, there were some taxonomic annotation discordances between the two tools.
If you want, I may send you my results.