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HMMER
User's Guide
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Dept. of Genetics |
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Subsections
hmmalign
[options] hmmfile seqfile
hmmalign reads an HMM file from
hmmfile and a set of sequences from seqfile, aligns the sequences to
the profile HMM, and outputs a multiple sequence alignment.
seqfile
may be in any unaligned or aligned file format accepted by HMMER. If it
is in a multiple alignment format (e.g. MSF, SELEX, ClustalW), the existing
alignment is ignored.
- [-h ] Print brief help; includes version
number and summary of all options, including expert options.
- [-m ] Include
in the alignment only those symbols aligned to match states. Do not show
symbols assigned to insert states.
- [-o <f> ] Save alignment to file <f> instead
of to standard output.
- [-q ] quiet; suppress all output except the alignment
itself. Useful for piping or redirecting the output.
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Direct comments and questions to <eddy@genetics.wustl.edu>