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

6       hmmstat - 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  read
22       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 profile in the file
29              starting 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  ex‐
52              pected (mean) score per consensus position. This is what the de‐
53              fault entropy-weighting method for effective sequence number es‐
54              timation  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 ac‐
65              count the transition (insertion/deletion) probabilities; it  may
66              be  a  more accurate estimation of the average score contributed
67              per model consensus position.
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70       compKL Kullback-Leibler divergence from  the  default  background  fre‐
71              quency  distribution to the average composition of the profile's
72              consensus match states, in bits.  The higher  this  number,  the
73              more  biased  the  residue composition of the profile is. Highly
74              biased profiles can slow the HMMER3  acceleration  pipeline,  by
75              causing too many nonhomologous 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 HM‐
91       MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
92       mer.org/).
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98       Copyright (C) 2020 Howard Hughes Medical Institute.
99       Freely distributed under the BSD open source license.
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101       For  additional  information  on  copyright and licensing, see the file
102       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
103       web page (http://hmmer.org/).
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AUTHOR

108       http://eddylab.org
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116HMMER 3.3.2                        Nov 2020                         hmmstat(1)
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