hmmstat - summary statistics for a profile file
hmmstat [options] hmmfile
The hmmstat utility prints out a tabular file of summary
statistics for each profile in hmmfile.
hmmfile may be '-' (a dash character), in which case
profiles are read from a stdin pipe instead of from a file.
The columns are:
- idx
- The index of this profile, numbering each profile in the file starting
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 calculation 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 contributed per model consensus position.
- compKL
- Kullback-Leibler divergence from the default background frequency
distribution to the average composition of the profile's consensus match
states, in bits. 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 nonhomologous sequences to pass
the filters.
- -h
- Help; print a brief reminder of command line usage and all available
options.
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
(http://hmmer.org/).
Copyright (C) 2020 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the
file called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page (http://hmmer.org/).