Contents

• Overview
  • What HMMs are
  • What HMMs can do for you
  • Programs
  • General notes on all the programs
  • Environment variables
• Tutorial
  • Building an HMM from an alignment: hmmb
  • Training an HMM on unaligned sequences: hmmt
    • Simulated annealing HMM training
    • Providing an existing alignment as a hint
  • Making multiple alignments: hmma
  • Searching sequence databases
    • Smith/Waterman searches: hmmsw
    • Searching for multiple Smith/Waterman hits: hmmfs
    • Global (Needleman/Wunsch) style searching: hmms
    • Local (Needleman/Wunsch) style searching: hmmls
  • Generating likely sequences: hmme
  • Decoding an HMM file: hmm-convert
• Advanced topics
  • Constrained simulated annealing
• 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...
• Acknowledgements
• References
• Distribution and copying terms
• File formats
  • Sequence files
    • Single sequence formats
    • Multiple unaligned sequences (databases)
    • Alignments
    • Warnings
    • FASTA unaligned sequence format
      • Example of a simple FASTA file
    • SELEX alignment format
      • Example of a simple SELEX format file
      • Detailed specification of a SELEX file
      • Optional annotation
      • Secondary structure
      • Reference coordinate system
      • Sequence header
      • Author
      • An example SELEX file with annotation
  • Prior files
• Installation instructions
• Release notes
  • 1.8
  • 1.7
  • 1.6
  • 1.5
• Manual pages
  • hmmer
  • hmma
  • hmmb
  • hmme
  • hmmfs
  • hmmls
  • hmms
  • hmmsw
  • hmmt
  • hmm-convert
• About this document ...