I've been using the GTDB tree/kraken 2 table recently. The genome IDs contain underscores in their names. When i import my table into QIIME as a
FeatureTable[Frequency] (so biom under the hood), the underscores in the name are preserved. When I import the tree (
Phylogeny[Rooted]) with tip IDs that contain underscores, the underscores are replaced by spaces. This may be a scikit-bio, python API specific quirk, but it's darn obnoxious. If it's more appropriate as a scikit-bio issue, I'm happy to take it there, but QIIME 2 is where the integration breaks.
Let me know if example code, etc would help; I'm happy to share.