1hmmconvert(1)                    HMMER Manual                    hmmconvert(1)
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NAME

6       hmmconvert - convert between profile HMM file formats
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SYNOPSIS

10       hmmconvert [options] oldhmmfile newhmmfile
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DESCRIPTION

14       hmmconvert  reads  an HMM file from oldhmmfile in any HMMER format, and
15       writes it to a new file newhmmfile in a  new  format.   oldhmmfile  and
16       newhmmfile  must  be  different files; you can't reliably overwrite the
17       old file.  By default, the new HMM file is written  in  HMMER  2  ASCII
18       format.
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20       Available  formats are HMMER 2 ASCII (default), HMMER 2 binary (-b) GCG
21       profile (-p) , and Compugen XSW extended profile (-P).
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OPTIONS

25       -a     Convert to HMMER 2 ASCII file. This  is  the  default,  so  this
26              option is unnecessary.
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29       -b     Convert to HMMER 2 binary file.
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32       -h     Print  brief  help;  includes  version number and summary of all
33              options, including expert options.
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36       -p     Convert to GCG profile .prf format.
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39       -A     Append mode; append to newhmmfile rather  than  creating  a  new
40              file.
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43       -F     Force; if newhmmfile already exists, and -A is not being used to
44              append to the file, hmmconvert will refuse to clobber the exist‐
45              ing file unless -F is used.
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48       -P     Convert  the  HMM to Compugen XSW extended profile format, which
49              is similar to GCG profile format but has two extra  columns  for
50              delete-open  and  delete-extend  costs.   (I do not believe that
51              Compugen publicly supports this format; it may be undocumented.)
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SEE ALSO

56       Master man page, with full list of and  guide  to  the  individual  man
57       pages: see hmmer(1).
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59       For  complete documentation, see the user guide that came with the dis‐
60       tribution   (Userguide.pdf);   or   see    the    HMMER    web    page,
61       http://hmmer.wustl.edu/.
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65       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
66       Freely distributed under the GNU General Public License (GPL).
67       See the file COPYING in your distribution for details on redistribution
68       conditions.
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AUTHOR

72       Sean Eddy
73       HHMI/Dept. of Genetics
74       Washington Univ. School of Medicine
75       4566 Scott Ave.
76       St Louis, MO 63110 USA
77       http://www.genetics.wustl.edu/eddy/
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83HMMER 2.3.2                        Oct 2003                      hmmconvert(1)
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