1hmmpress(1)                      HMMER Manual                      hmmpress(1)
2
3
4

NAME

6       hmmpress - prepare an HMM database for hmmscan
7
8

SYNOPSIS

10       hmmpress [options] <hmmfile>
11
12
13

DESCRIPTION

15       Starting  from  a profile database <hmmfile> in standard HMMER3 format,
16       construct binary compressed datafiles for hmmscan.  The  hmmpress  step
17       is required for hmmscan to work.
18
19
20       Four  files  are  created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f,
21       and <hmmfile>.h3p.  The <hmmfile>.h3m file contains  the  profile  HMMs
22       and  their annotation in a binary format.  The <hmmfile>.h3i file is an
23       SSI index for the <hmmfile>.h3m file.  The <hmmfile>.h3f file  contains
24       precomputed data structures for the fast heuristic filter (the MSV fil‐
25       ter).  The <hmmfile>.h3p file contains precomputed data structures  for
26       the rest of each profile.
27
28
29       <hmmfile>  may  not be '-' (dash); running hmmpress on a standard input
30       stream rather than a file is not allowed.
31
32
33

OPTIONS

35       -h     Help; print a brief reminder  of  command  line  usage  and  all
36              available options.
37
38
39       -f     Force;   overwrites  any  previous  hmmpress'ed  datafiles.  The
40              default is to bitch about any existing  files  and  ask  you  to
41              delete them first.
42
43
44
45
46

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.
50
51
52       For complete documentation, see the user  guide  that  came  with  your
53       HMMER distribution (Userguide.pdf); or see the HMMER web page ().
54
55
56
57

59       Copyright (C) 2015 Howard Hughes Medical Institute.
60       Freely distributed under the GNU General Public License (GPLv3).
61
62       For  additional  information  on  copyright and licensing, see the file
63       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
64       web page ().
65
66
67

AUTHOR

69       Eddy/Rivas Laboratory
70       Janelia Farm Research Campus
71       19700 Helix Drive
72       Ashburn VA 20147 USA
73       http://eddylab.org
74
75
76
77HMMER 3.1b2                      February 2015                     hmmpress(1)
Impressum