pkg-descr

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.

WWW: http://hmmer.wustl.edu/

pkg-message

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HMMER reads three optional environment variables:
HMMERDB - directory location of HMM databases (e.g. PFAM)
BLASTDB - directory location of FASTA-formatted sequence databases
BLASTMAT - directory location of PAM scoring matrices

The BLASTDB and BLASTMAT variables are shared with versions of BLAST such
as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port). If these
variables are set, you do not have to specify the full path to your
databases on the command line when using HMMER.

Please see the documentation for more information.
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pkg-plist

bin/hmmalign
bin/hmmbuild
bin/hmmcalibrate
bin/hmmconvert
bin/hmmemit
bin/hmmfetch
bin/hmmindex
bin/hmmpfam
bin/hmmsearch
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