grappa 2.0 biology =0

Genome Rearrangements Analysis and Phylogeny Software

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: 04 Jul 2001 05:39:40
License: not specified in port

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GRAPPA: Genome Rearrangements Analysis under Parsimony and other
Phylogenetic Algorithms
				     
This suite of programs implements the approach to phylogeny
reconstruction from gene orders described in the paper
   Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M.,
   ``A detailed study of breakpoint analysis,''
   Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001).
In its current state, "grappa" allows one to explore either the
space of all possible trees on n labelled leaves or the space of all
such trees that obey (are refinements of) a particular constraint tree.

"invdist" takes the first two genomes in the input file and returns
their inversion distance.
"distmat" prints the inversion and breakpoint distance matrices. 

WWW: http://www.cs.unm.edu/~moret/GRAPPA/

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Build: devel/gmake
There are no ports dependent upon this port

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

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Configuration Options

     No options to configure

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Master Sites:

http://www.cs.unm.edu/~moret/GRAPPA/

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

Update to GNU make 3.82 after numerous -exp runs.

- Get Rid MD5 support

Reset dbader@ece.unm.edu due to timeouts and no response to email.

Hat:            portmgr

Remove USE_REINPLACE from all categories starting with B

SHA256ify

Approved by:    krion@

- update grappa to 2.0
- utilize PLIST_FILES
- unbreak it on 4.x
- update maintainer's email

PR:             79241
Submitted by:   David A. Bader <dbader@ece.unm.edu>

This is now buildable on 5.x, remove BROKEN.

SIZEify (maintainer timeout)

Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)

Mark as broken on 5.x due to the usual gcc terminating-character hassles.
Notified mainatainer.

De-pkg-comment.

- Update to version 1.0.3    

Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny   Software.    

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