[WashU] HMMER
User's Guide


| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC|
| Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

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Subsections

hmmalign - align sequences to an HMM profile

Synopsis

hmmalign [options] hmmfile seqfile

Description

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.

Options

Expert Options


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Next: hmmbuild - build a Up: Manual pages Previous: HMMER - profile hidden


Direct comments and questions to <eddy@genetics.wustl.edu>