1hmmcalibrate(1) HMMER Manual hmmcalibrate(1)
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6 hmmcalibrate - calibrate HMM search statistics
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10 hmmcalibrate [options] hmmfile
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14 hmmcalibrate reads an HMM file from hmmfile, scores a large number of
15 synthesized random sequences with it, fits an extreme value distribu‐
16 tion (EVD) to the histogram of those scores, and re-saves hmmfile now
17 including the EVD parameters.
18 hmmcalibrate may take several minutes (or longer) to run. While it is
21 running, a temporary file called hmmfile.xxx is generated in your work‐
22 ing directory. If you abort hmmcalibrate prematurely (ctrl-C, for
23 instance), your original hmmfile will be untouched, and you should
24 delete the hmmfile.xxx temporary file.
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28 -h Print brief help; includes version number and summary of all
29 options, including expert options.
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33 --cpu <n>
34 Sets the maximum number of CPUs that the program will run on.
35 The default is to use all CPUs in the machine. Overrides the
36 HMMER_NCPU environment variable. Only affects threaded versions
37 of HMMER (the default on most systems).
38 --fixed <n>
41 Fix the length of the random sequences to <n>, where <n> is a
42 positive (and reasonably sized) integer. The default is instead
43 to generate sequences with a variety of different lengths, con‐
44 trolled by a Gaussian (normal) distribution.
45 --histfile <f>
48 Save a histogram of the scores and the fitted theoretical curve
49 to file <f>.
50 --mean <x>
53 Set the mean length of the synthetic sequences to <x>, where <x>
54 is a positive real number. The default is 350.
55 --num <n>
58 Set the number of synthetic sequences to <n>, where <n> is a
59 positive integer. If <n> is less than about 1000, the fit to the
60 EVD may fail. Higher numbers of <n> will give better determined
61 EVD parameters. The default is 5000; it was empirically chosen
62 as a tradeoff between accuracy and computation time.
63 --pvm Run on a Parallel Virtual Machine (PVM). The PVM must already be
66 running. The client program hmmcalibrate-pvm must be installed
67 on all the PVM nodes. Optional PVM support must have been com‐
68 piled into HMMER.
69 --sd <x>
72 Set the standard deviation of the synthetic sequence length dis‐
73 tribution to <x>, where <x> is a positive real number. The
74 default is 350. Note that the Gaussian is left-truncated so that
75 no sequences have lengths <= 0.
76 --seed <n>
79 Set the random seed to <n>, where <n> is a positive integer. The
80 default is to use time() to generate a different seed for each
81 run, which means that two different runs of hmmcalibrate on the
82 same HMM will give slightly different results. You can use this
83 option to generate reproducible results for different hmmcali‐
84 brate runs on the same HMM.
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89 Master man page, with full list of and guide to the individual man
90 pages: see hmmer(1).
91 For complete documentation, see the user guide that came with the dis‐
93 tribution (Userguide.pdf); or see the HMMER web page,
94 http://hmmer.wustl.edu/.
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98 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
99 Freely distributed under the GNU General Public License (GPL).
100 See the file COPYING in your distribution for details on redistribution
101 conditions.
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105 Sean Eddy
106 HHMI/Dept. of Genetics
107 Washington Univ. School of Medicine
108 4566 Scott Ave.
109 St Louis, MO 63110 USA
110 http://www.genetics.wustl.edu/eddy/
111HMMER 2.3.2 Oct 2003 hmmcalibrate(1)