1hmmstat(1)                       HMMER Manual                       hmmstat(1)
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NAME

6       hmmstat - display summary statistics for a profile file
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SYNOPSIS

11       hmmstat [options] <hmmfile>
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DESCRIPTION

16       The hmmstat utility prints out a tabular file of summary statistics for
17       each profile in <hmmfile>.
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21       <hmmfile> may be '-' (a dash character), in  which  case  profiles  are
22       read from a <stdin> pipe instead of from a file.
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25       The columns are:
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28       idx    The  index of this profile, numbering each on in the file start‐
29              ing from 1.
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32       name   The name of the profile.
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35       accession
36              The optional accession of the profile, or "-" if there is none.
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39       nseq   The number of sequences that the profile was estimated from.
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42       eff_nseq
43              The effective number of sequences that the profile was estimated
44              from,  after HMMER applied an effective sequence number calcula‐
45              tion such as the default entropy weighting.
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48       M      The length of the model in consensus residues (match states).
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51       relent Mean relative entropy per match state,  in  bits.  This  is  the
52              expected  (mean)  score per consensus position. This is what the
53              default entropy-weighting method for effective  sequence  number
54              estimation  focuses on, so for default HMMER3 models, you expect
55              this value to reflect the default target for entropy-weighting.
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58       info   Mean information content per match state, in bits.  Probably not
59              useful.  Information content is a slightly different calculation
60              than relative entropy.
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63       p relE Mean positional relative entropy, in bits.  This  is  a  fancier
64              version  of  the  per-match-state  relative entropy, taking into
65              account the transition  (insertion/deletion)  probabilities;  it
66              may  be a more accurate estimation of the average score contrib‐
67              uted per model consensus position.
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70       compKL Kullback-Leibler distance between the  model's  overall  average
71              residue composition and the default background frequency distri‐
72              bution.  The higher this number, the  more  biased  the  residue
73              composition  of  the profile is. Highly biased profiles can slow
74              the HMMER3 acceleration pipeline, by causing too many nonhomolo‐
75              gous sequences to pass the filters.
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OPTIONS

80       -h     Help;  print  a  brief  reminder  of  command line usage and all
81              available options.
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SEE ALSO

86       See hmmer(1) for a master man page with a list of  all  the  individual
87       man pages for programs in the HMMER package.
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90       For  complete  documentation,  see  the  user guide that came with your
91       HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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97       Copyright (C) 2015 Howard Hughes Medical Institute.
98       pFreely distributed under the GNU General Public License (GPLv3).
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100       For additional information on copyright and  licensing,  see  the  file
101       called  COPYRIGHT  in  your HMMER source distribution, or see the HMMER
102       web page ().
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AUTHOR

107       Eddy/Rivas Laboratory
108       Janelia Farm Research Campus
109       19700 Helix Drive
110       Ashburn VA 20147 USA
111       http://eddylab.org
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119HMMER 3.1b2                      February 2015                      hmmstat(1)
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