I would like to ask you how to compare proteome files in Pfam database by using Hmmer program. I have 2 species proteome files and I would like to compare these two species` proteome files to other proteome files (10 files) I selected. I read hmmer manual but I am little confused. For instance, the manual says an alignment file. For this, should I align all species proteome files (12) in a file and then use? On the other hand, as far as I understand, firstly I have to use some hmmer programs (hmmpress etc.) before hmmscan and build a database? Actually, a clear flowchart would be so helpful, as I am quite new on this area.