| hmmalign | Align sequences to an HMM profile. |
| hmmalign [options] hmmfile seqfile | | Options - -h
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Print brief help; includes version number and summary of all options, including expert options. - -m
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Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. - -o f
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Save alignment to file f instead of to standard output. - -q
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Quiet; suppress all output except the alignment itself. |