[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 |

next up previous contents
Next: hmmconvert - convert between Up: Manual pages Previous: hmmbuild - build a

Subsections

hmmcalibrate - calibrate HMM search statistics

Synopsis

hmmcalibrate [options] hmmfile

Description

hmmcalibrate reads an HMM file from hmmfile, scores a large number of synthesized random sequences with it, fits an extreme value distribution (EVD) to the histogram of those scores, and re-saves hmmfile now including the EVD parameters.

hmmcalibrate may take several minutes (or longer) to run. While it is running, a temporary file called hmmfile.xxx is generated in your working directory. If you abort hmmcalibrate prematurely (ctrl-C, for instance), your original hmmfile will be untouched, and you should delete the hmmfile.xxx temporary file.

Options

Expert Options


next up previous contents
Next: hmmconvert - convert between Up: Manual pages Previous: hmmbuild - build a


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