wise 2.2.0 biology =1

Intelligent algorithms for DNA searches

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
Port Added: 10 Sep 2002 13:59:05
License: not specified in port

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"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)

WWW: http://www.ebi.ac.uk/Wise2/

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMonThere are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/wise/ && make install clean
To add the package: pkg_add -r wise

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Configuration Options

     No options to configure

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Master Sites:

ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Get Rid MD5 support

Fix plist.

Reported by:    QAT

- SBU_FILES += pkg-message

PR:             ports/142409
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>

Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:            portmgr

Remove USE_REINPLACE from all categories starting with B

SHA256ify

Approved by:    krion@

Fix maintainer address

    From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    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 <anthony.maher@uts.edu.au>

SIZEify (maintainer timeout)

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

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 <tonymaher@optushome.com.au>

De-pkg-comment.

Add missing file

Modify replace RE to match syntax of sed now ("\)" -> ")"
Noticed by: bento

PERL -> REINPLACE
And some ports have USE_PERL5=yes now.

"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."

12 vulnerabilities affecting 17 ports have been reported in the past 14 days

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