Frequently Asked Questions

• What HMMs are available?
• What do HMM scores mean?
• My HMM doesn't recognize these known homologues!
• My HMM makes lousy alignments!
• Can I keep some of an alignment fixed?
• I can't get HMMER to work at all...
• My HMM built on machine X can't be read on machine Y...
• hmmt simulated annealing says ``SA trace crash....''
• Where's a chapter or two on the advanced features?
• The program crashed. What do I do?
• If HMMER did X, I would be sooo happy...