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This is the command hmmstat that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



hmmstat - display 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> 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 on in the file starting from 1.

name The name of the profile.

The optional accession of the profile, or "-" if there is none.

nseq 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

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 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.


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

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