1hmmpress(1)                      HMMER Manual                      hmmpress(1)
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NAME

6       hmmpress - prepare a profile database for hmmscan
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SYNOPSIS

10       hmmpress [options] hmmfile
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DESCRIPTION

15       Constructs  binary  compressed  datafiles  for hmmscan, starting from a
16       profile database hmmfile in standard HMMER3 format.  The hmmpress  step
17       is required for hmmscan to work.
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20       Four files are created: hmmfile.h3m, hmmfile.h3i, hmmfile.h3f, and hmm‐
21       file.h3p.  The hmmfile.h3m file contains the profile HMMs and their an‐
22       notation  in a binary format.  The hmmfile.h3i file is an SSI index for
23       the hmmfile.h3m file.  The hmmfile.h3f file contains  precomputed  data
24       structures  for  the  fast heuristic filter (the MSV filter).  The hmm‐
25       file.h3p file contains precomputed data structures for the rest of each
26       profile.
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29       hmmfile  may  not  be  '-' (dash); running hmmpress on a standard input
30       stream rather than a file is not allowed.
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OPTIONS

35       -h     Help; print a brief reminder  of  command  line  usage  and  all
36              available options.
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39       -f     Force;  overwrites  any  previous hmmpress'ed datafiles. The de‐
40              fault is to bitch about any existing files and ask you to delete
41              them first.
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SEE ALSO

48       See  hmmer(1)  for  a master man page with a list of all the individual
49       man pages for programs in the HMMER package.
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52       For complete documentation, see the user guide that came with your  HM‐
53       MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
54       mer.org/).
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60       Copyright (C) 2020 Howard Hughes Medical Institute.
61       Freely distributed under the BSD open source license.
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63       For additional information on copyright and  licensing,  see  the  file
64       called  COPYRIGHT  in  your HMMER source distribution, or see the HMMER
65       web page (http://hmmer.org/).
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AUTHOR

70       http://eddylab.org
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74HMMER 3.3.2                        Nov 2020                        hmmpress(1)
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