|
HMMER
User's Guide
|
|
Dept. of Genetics |
WashU |
Medical School |
Sequencing Center |
CGM |
IBC|
|
Eddy lab |
Internal (lab only) |
HMMER |
PFAM |
tRNAscan-SE |
Software |
Publications
|
Next: Files used in the
Up: Tutorial
Previous: Tutorial
There are currently seven programs supported in the beta release of 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.
- hmmpfam
- Search an HMM database for matches to a query sequence.
- hmmsearch
- Search a sequence database for matches to an HMM.
The following four programs are not included in the initial beta
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.
Next: Files used in the
Up: Tutorial
Previous: Tutorial
Direct comments and questions to <eddy@genetics.wustl.edu>