@Evangelos Karatzas Hello! Please a I need a little of help I deactivate HMMER sequence recruitment. I used --min-seq-id 0.8 -c 0.9 --cov-mode 0, then I did a all-vs-all alignment with BLASTP of the representative sequences and I found that some sequences have 100% cover (similar size) and 81% identity. Weren't these sequences supposed to be grouped together? What am i missing here? Maybe do you know the reason of this behavior? Thanks!