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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19       The columns are:
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22       idx    The index of this profile, numbering each on in the file  start‐
23              ing from 1.
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26       name   The name of the profile.
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29       accession
30              The optional accession of the profile, or "-" if there is none.
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33       nseq   The number of sequences that the profile was estimated from.
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36       eff_nseq
37              The effective number of sequences that the profile was estimated
38              from, after HMMER applied an effective sequence number  calcula‐
39              tion such as the default entropy weighting.
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42       M      The length of the model in consensus residues (match states).
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45       relent Mean  relative  entropy  per  match  state, in bits. This is the
46              expected (mean) score per consensus position. This is  what  the
47              default  entropy-weighting  method for effective sequence number
48              estimation focuses on, so for default HMMER3 models, you  expect
49              this value to reflect the default target for entropy-weighting.
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52       info   Mean information content per match state, in bits.  Probably not
53              useful. Information content is a slightly different  calculation
54              than relative entropy.
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57       p relE Mean  positional  relative  entropy, in bits.  This is a fancier
58              version of the per-match-state  relative  entropy,  taking  into
59              account  the  transition  (insertion/deletion) probabilities; it
60              may be a more accurate estimation of the average score  contrib‐
61              uted per model consensus position.
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64       compKL Kullback-Leibler  distance  between  the model's overall average
65              residue composition and the default background frequency distri‐
66              bution.   The  higher  this  number, the more biased the residue
67              composition of the profile is. Highly biased profiles  can  slow
68              the HMMER3 acceleration pipeline, by causing too many nonhomolo‐
69              gous sequences to pass the filters.
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OPTIONS

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

80       See  hmmer(1)  for  a master man page with a list of all the individual
81       man pages for programs in the HMMER package.
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84       For complete documentation, see the user  guide  that  came  with  your
85       HMMER   distribution   (Userguide.pdf);  or  see  the  HMMER  web  page
86       (@HMMER_URL@).
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92       @HMMER_COPYRIGHT@
93       p@HMMER_LICENSE@
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95       For additional information on copyright and  licensing,  see  the  file
96       called  COPYRIGHT  in  your HMMER source distribution, or see the HMMER
97       web page (@HMMER_URL@).
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AUTHOR

102       Eddy/Rivas Laboratory
103       Janelia Farm Research Campus
104       19700 Helix Drive
105       Ashburn VA 20147 USA
106       http://eddylab.org
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114HMMER @HMMER_VERSION@            @HMMER_DATE@                       hmmstat(1)
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