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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 ...
Sean Eddy
Mon Apr 17 09:54:19 CDT 1995