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1.2
date	2001.07.05.08.58.12;	author wjv;	state Exp;
branches;
next	1.1;

1.1
date	98.07.12.23.30.04;	author steve;	state Exp;
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	1.1.1.1;
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1.1.1.1
date	98.07.12.23.30.04;	author steve;	state Exp;
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desc
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1.2
log
@- General clean-up of port.
- Install PDF and HTML documentation.
- Take over maintainership.

Approved by:	Silence from previous maintainer; no objections from -ports
@
text
@---------------------------------------------------------------------------
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.
---------------------------------------------------------------------------
@


1.1
log
@Initial revision
@
text
@d1 5
a5 1
*********************************************************
d7 4
a10 1
Note on environment variables:
d12 2
a13 18
   HMMER reads three 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

   If you have installed BLAST, you probably already have these 
   environment variables set in system-wide or user-specific
   .cshrc files. They are optional. If they are set up, you
   can simplify command lines to:
      > hmmpfam pfam my.query
      > hmmsearch my.hmm swiss35
   instead of
      > hmmpfam   /some/long/path/to/databases/pfam my.query
      > hmmsearch my.hmm /some/long/path/to/databases/swiss35

Please see the website http://hmmer.wustl.edu/ for more information.

*********************************************************
@


1.1.1.1
log
@Initial import of hmmer version 2.0.
Profile hidden Markov models for biological sequence analysis.

PR:		7120
Submitted by:	Matthew Jason Euclid Barnhart <barnhart@@sequencer.wustl.edu>
@
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