hmmcalibrate.man

hmmer源程序

.TH "hmmcalibrate" 1 @RELEASEDATE@ "HMMER @RELEASE@" "HMMER Manual"

.SH NAME
.TP 
hmmcalibrate - calibrate HMM search statistics

.SH SYNOPSIS
.B hmmcalibrate
.I [options]
.I hmmfile

.SH DESCRIPTION

.B hmmcalibrate
reads an HMM file from
.I 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
.I hmmfile
now including the EVD parameters.

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

.SH OPTIONS

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

.SH EXPERT OPTIONS

.TP
.BI --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).

.TP
.BI --fixed " <n>"
Fix the length of the random sequences to
.I <n>,
where 
.I <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.

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

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

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

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

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

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

.SH SEE ALSO

.PP
Master man page, with full list of and guide to the individual man
pages: see 
.B hmmer(1).
.PP
A User guide and tutorial came with the distribution:
.B Userguide.ps
[Postscript] and/or
.B Userguide.pdf
[PDF].
.PP
Finally, all documentation is also available online via WWW: 
.B http://hmmer.wustl.edu/

.SH AUTHOR

This software and documentation is: 
.nf
@COPYRIGHT@
HMMER - Biological sequence analysis with profile HMMs
Copyright (C) 1992-1999 Washington University School of Medicine
All Rights Reserved

    This source code is distributed under the terms of the
    GNU General Public License. See the files COPYING and LICENSE
    for details.
.fi
See the file COPYING in your distribution for complete details.

.nf
Sean Eddy
HHMI/Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA
Phone: [phone]
FAX  : [phone]
Email: [e-mail]
.fi