[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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Next: hmmcalibrate - calibrate HMM Up: Manual pages Previous: hmmalign - align sequences

Subsections

hmmbuild - build a profile HMM from an alignment

Synopsis

hmmbuild [options] hmmfile alignfile

Description

hmmbuild reads a multiple sequence alignment file alignfile , builds a new profile HMM, and saves the HMM in hmmfile.

alignfile may be in ClustalW, GCG MSF, or SELEX alignment format.

By default, the model is configured to find one or more nonoverlapping alignments to the complete model. This is analogous to the behavior of the hmmls program of HMMER 1. To configure the model for a single global alignment, use the -g option; to configure the model for multiple local alignments a la the old program hmmfs, use the -f option; and to configure the model for a single local alignment (a la standard Smith/Waterman, or the old hmmsw program), use the -s option.

Options

Expert Options


next up previous contents
Next: hmmcalibrate - calibrate HMM Up: Manual pages Previous: hmmalign - align sequences


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