Hello, and thank you for developing and maintaining BAQLaVa.
I am currently working on phage lifestyle classification (temperate, virulent, or unclassified) using BAQLaVa-derived VGBs, and I would be very grateful for your advice on one point.
My main difficulty is that a single VGB can be associated with multiple BAQ reference sequences, and BACPHLIP predictions across those reference sequences are not always consistent. In some cases, different BAQ sequences linked to the same VGB receive different lifestyle predictions.
Because of this, my question is not so much how to interpret an individual BAQ sequence, but rather how to define a representative lifestyle classification at the VGB level when BAQ-level predictions are discordant.
In this situation, could you kindly advise on the most biologically reasonable and defensible way to assign a single lifestyle label to a VGB? For example, would you recommend using a majority-based approach, prioritizing higher-quality reference sequences, or taking a more conservative approach and leaving such VGBs as unclassified?
I would greatly appreciate any guidance you may have. Thank you very much for your time and help.
Seoul national university
min-uk Park