HMMER User's Guide

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The programs in HMMER

There are currently nine programs supported in the HMMER 2 package:

hmmalign

Align sequences to an existing model.

hmmbuild

Build a model from a multiple sequence alignment.

hmmcalibrate

Takes an HMM and empirically determines parameters that are used to make searches more sensitive, by calculating more accurate expectation value scores (E-values).

hmmconvert

Convert a model file into different formats, including a compact HMMER 2 binary format, and ``best effort'' emulation of GCG profiles.

hmmemit

Emit sequences probabilistically from a profile HMM.

hmmfetch

Get a single model from an HMM database.

hmmindex

Index an HMM database.

hmmpfam

Search an HMM database for matches to a query sequence.

hmmsearch

Search a sequence database for matches to an HMM.

HMMER also provides a number of utility programs which are not HMM programs, but may be useful:

alistat

Show some simple statistics about a sequence alignment file.

getseq

Retrieve a (sub-)sequence from a sequence file.

seqstat

Show some simple statistics about a sequence file.

sreformat

Reformat a sequence file into a different format.

The following four programs are not included in the current release, but are planned (i.e. they're vaporware, but it may be useful to you to know that they're on the drawing board:)

hmmconfig

Alter the search configuration of an existing model.

hmminfo

Display summary information about the model(s) in a file.

hmmtrain

Train a model from initially unaligned sequences, producing both a model and a multiple alignment.

hmmview

Graphical viewer and editor for HMMs.