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hmm2calibrate - calibrate HMM search statistics


hmm2calibrate [options] hmmfile


hmm2calibrate 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.

hmm2calibrate 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
hmm2calibrate prematurely (ctrl-C, for instance), your original hmmfile will be untouched,
and you should delete the hmmfile.xxx temporary file.


-h Print brief help; includes version number and summary of all options, including
expert options.


--cpu <n>
Sets the maximum number of CPUs that the program will run on. The default is to use
all CPUs in the machine. Overrides the HMMER_NCPU environment variable. Only
affects threaded versions of HMMER (the default on most systems).

--fixed <n>
Fix the length of the random sequences to <n>, where <n> is a positive (and
reasonably sized) integer. The default is instead to generate sequences with a
variety of different lengths, controlled by a Gaussian (normal) distribution.

--histfile <f>
Save a histogram of the scores and the fitted theoretical curve to file <f>.

--mean <x>
Set the mean length of the synthetic sequences to <x>, where <x> is a positive real
number. The default is 350.

--num <n>
Set the number of synthetic sequences to <n>, where <n> is a positive integer. If
<n> is less than about 1000, the fit to the EVD may fail. Higher numbers of <n>
will give better determined EVD parameters. The default is 5000; it was empirically
chosen as a tradeoff between accuracy and computation time.

--pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The
client program hmm2calibrate-pvm must be installed on all the PVM nodes. Optional
PVM support must have been compiled into HMMER.

--sd <x>
Set the standard deviation of the synthetic sequence length distribution to <x>,
where <x> is a positive real number. The default is 350. Note that the Gaussian is
left-truncated so that no sequences have lengths <= 0.

--seed <n>
Set the random seed to <n>, where <n> is a positive integer. The default is to use
time() to generate a different seed for each run, which means that two different
runs of hmm2calibrate on the same HMM will give slightly different results. You
can use this option to generate reproducible results for different hmm2calibrate
runs on the same HMM.

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