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hmmer

profile hidden Markov models for protein sequence analysis

Variants:
HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries.

Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family.

Homepage:
Package version:3.0-4
Architecture:s390x
Distribution:Debian
Filename:hmmer_3.0-4_s390x.deb

/usr/share/doc/hmmer/README

HMMER - profile hidden Markov models for biological sequence analysis
http://hmmer.org/
Version 3.0; March 2010
Copyright (C) 2010 Howard Hughes Medical Institute.
------------------------------------------------------------------

HMMER searches biological sequence databases for homologous sequences,
using either single sequences or multiple sequence alignments as
queries. HMMER implements a tech
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/usr/share/doc/hmmer/README.Debian

hmmer for Debian
----------------

This is now version 3.0 of HMMER which is real nice
and should substitute the 2.3 version. 

Support of MPI is now available, even though this
package does not offer it yet. The PVM of version 2.3
is no longer supported by upstream and not shipping
any longer with Debian.

The packaging is lintian-clean, albeit not perfect.

Steffen and Eric at the BOSC Codefest 
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/usr/share/man/man1/hmmalign.1.gz

hmmalign(1)                 HMMER Manual                 hmmalign(1)



NAME
       hmmalign - align sequences to a profile HMM


SYNOPSIS
       hmmalign [options] <hmmfile> <seqfile>


DESCRIPTION
       Perform a multiple sequence alignment of all the sequences in
       seqfile, by aligning them individually to the profile HMM  in
       hmmfile.


       The new alignment is output to stdout 
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/usr/share/man/man1/hmmbuild.1.gz

hmmbuild(1)                 HMMER Manual                 hmmbuild(1)



NAME
       hmmbuild  -  con
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/usr/share/man/man1/hmmconvert.1.gz

hmmconvert(1)               HMMER Manual               hmmconvert(1)



NAME
       hmmconvert - con
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/usr/share/man/man1/hmmemit.1.gz

hmmemit(1)                  HMMER Manual                  hmmemit(1)



NAME
       hmmemit - sample
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/usr/share/man/man1/hmmer.1.gz

HMMER(1)                    HMMER Manual                    HMMER(1)



NAME
       HMMER - profile 
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/usr/share/man/man1/hmmfetch.1.gz

hmmfetch(1)                 HMMER Manual                 hmmfetch(1)



NAME
       hmmfetch - retri
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