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HMMER - profile hidden Markov models for biological sequence analysis
Version 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
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o About this software...
HMMER is an implementation of profile HMM methods for
sensitive database searches using multiple sequence alignments as queries.
Basically, you give HMMER a multiple sequence alignment as input;
it builds a statistical model called a "hidden Markov model"
which you can then use as a query into a sequence database
to find (and/or align) additional homologues of the sequence family.
o Getting HMMER
WWW home: http://hmmer.janelia.org/
Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
User's Guide: ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf
o Installing HMMER
See the file INSTALL for brief instructions.
See the chapter Installation in the HMMER User's Guide (Userguide.pdf)
for more detailed instructions.
See the file NOTES for notes particular to this release.
You should also read the following files:
COPYING -- copyright notice, and information on the free software license
LICENSE -- Full text of the GNU Public License, version 2 (see COPYING)
If you have obtained HMMER from Washington University under
a non-GPL license as part of a special licensing agreement,
COPYING and LICENSE will refer to the terms of that agreement.
o Getting started with HMMER
See the Tutorial section of the User's Guide (Userguide.pdf)
for a quick introduction to how to use HMMER.
o Registering HMMER
Email eddy@genetics.wustl.edu to register and get on my
very infrequent mailing list of HMMER news, patches, and updates.
o Reporting bugs
These programs are under active development. Though this
release has been tested and appears to be stable, bugs may crop up. If
you use these programs, please help me out and e-mail me with
suggestions, comments, and bug reports. (eddy@genetics.wustl.edu)
Sean Eddy
Howard Hughes Medical Institute and Dept. of Genetics
Washington University School of Medicine, St. Louis, Missouri, USA
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