The FreeBSD Ports Archive

FreeBSD biology : wise

Intelligent algorithms for DNA searches

 "Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns. This really is a rewrite of the old wisetools
package, which I wrote about 3 years ago.

It can compare a single protein or a profile HMM to a genomic DNA
sequence, and predict a gene structure. This is algorithm, called
genewise, is one of the algorithms available in Wise2. There are
other algorithms focused on EST data rather than genomic data, as
well as some other algorithm curios."
- from the web site (Ewan Birney) 

wise history

v. 1.8
date: 2006/12/26 12:46:33;  author: linimon;  state: Exp;  lines: +1 -1
Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:		portmgr

v. 1.7
date: 2006/05/03 23:26:35;  author: edwin;  state: Exp;  lines: +0 -1
Remove USE_REINPLACE from all categories starting with B

v. 1.6
date: 2006/01/09 03:25:02;  author: edwin;  state: Exp;  lines: +1 -1
Fix maintainer address

    From: Tony Maher 
    To: Edwin Groothuis 
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:	Tony Maher 

v. 1.5
date: 2003/09/24 11:32:44;  author: edwin;  state: Exp;  lines: +1 -1
Port update (maintainer): biology/wise

	Fenner's porsurvey show wise no longer available at original
	site.  Original site readme shows it has moved so update
	the MASTER_SITES accordingly.

PR:		ports/57154
Submmited by:	Tony Maher 

v. 1.4
date: 2003/02/21 11:01:38;  author: knu;  state: Exp;  lines: +1 -0
De-pkg-comment.

v. 1.3
date: 2002/11/05 01:44:12;  author: edwin;  state: Exp;  lines: +8 -8
Modify replace RE to match syntax of sed now ("\)" -> ")"
Noticed by: bento

v. 1.2
date: 2002/11/04 05:46:26;  author: edwin;  state: Exp;  lines: +5 -4
PERL -> REINPLACE
And some ports have USE_PERL5=yes now.

v. 1.1
date: 2002/09/10 13:58:40;  author: dinoex;  state: Exp;
"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."
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