hmmstat(1) HMMER Manual hmmstat(1)NAMEhmmstat - display summary statistics for a profile file
SYNOPSIShmmstat [options] <hmmfile>
DESCRIPTION
The hmmstat utility prints out a tabular file of summary statistics for
each profile in <hmmfile>.
The columns are:
idx The index of this profile, numbering each on in the file start‐
ing from 1.
name The name of the profile.
accession
The optional accession of the profile, or "-" if there is none.
nseq The number of sequences that the profile was estimated from.
eff_nseq
The effective number of sequences that the profile was estimated
from, after HMMER applied an effective sequence number calcula‐
tion such as the default entropy weighting.
M The length of the model in consensus residues (match states).
relent Mean relative entropy per match state, in bits. This is the
expected (mean) score per consensus position. This is what the
default entropy-weighting method for effective sequence number
estimation focuses on, so for default HMMER3 models, you expect
this value to reflect the default target for entropy-weighting.
info Mean information content per match state, in bits. Probably not
useful. Information content is a slightly different calculation
than relative entropy.
p relE Mean positional relative entropy, in bits. This is a fancier
version of the per-match-state relative entropy, taking into
account the transition (insertion/deletion) probabilities; it
may be a more accurate estimation of the average score contrib‐
uted per model consensus position.
compKL Kullback-Leibler distance between the model's overall average
residue composition and the default background frequency distri‐
bution. The higher this number, the more biased the residue
composition of the profile is. Highly biased profiles can slow
the HMMER3 acceleration pipeline, by causing too many nonhomolo‐
gous sequences to pass the filters.
OPTIONS-h Help; print a brief reminder of command line usage and all
available options.
SEE ALSO
See hmmer(1) for a master man page with a list of all the individual
man pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
(@HMMER_URL@).
COPYRIGHT
@HMMER_COPYRIGHT@
p@HMMER_LICENSE@
For additional information on copyright and licensing, see the file
called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page (@HMMER_URL@).
AUTHOR
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
HMMER @HMMER_VERSION@ @HMMER_DATE@ hmmstat(1)
