SYNOPSIShmmstat [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:
The index of this profile, numbering each on in the file starting from 1.
The name of the profile.
The optional accession of the profile, or "-" if there is none.
The number of sequences that the profile was estimated from.
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.
The length of the model in consensus residues (match states).
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.
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.
Kullback-Leibler distance between the model's overall average
residue composition and the default background frequency distribution.
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.
Help; print a brief reminder of command line usage and all available
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