General Linux Documentation:
To run this software interactively
in a Linux environment
run the commands:
module load hmmer
hmmbuild [-options] hmmout.file align.file
This will build a profile HMM (hmmout.file) from an input alignment file (align.file).
For a complete list of options, use the -h option, e.g.,
Other programs available in HMMER are:
- phmmer - Search a sequence against a sequence database.
- jackhmmer - Iteratively search a sequence against a sequence database.
- hmmbuild - Build a profile HMM from an input multiple alignment.
- hmmsearch - Search a profile HMM against a sequence database.
- hmmscan - Search a sequence against a profile HMM database.
- hmmalign - Make a multiple alignment of many sequences to a common profile HMM.
- hmmconvert - Convert profile formats to/from HMMER3 format.
- hmmemit - Generate sequences from a profile HMM.
- hmmfetch - Get a profile HMM by name or accession from an HMM database.
- hmmpress - Format an HMM database into a binary format for hmmscan.
- hmmstat - Show summary statistics for each profile in an HMM database.
For instructions on how to use each of these, use the -h option in the command line or visit the HMMER homepage.