The FreeBSD Ports Archive

FreeBSD biology : grappa

Genome Rearrangements Analysis and Phylogeny Software

 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.  

grappa history

v. 1.9
date: 2006/12/13 13:20:20;  author: linimon;  state: Exp;  lines: +1 -1
Reset dbader@ece.unm.edu due to timeouts and no response to email.

Hat:		portmgr

v. 1.8
date: 2006/05/03 23:26:33;  author: edwin;  state: Exp;  lines: +0 -1
Remove USE_REINPLACE from all categories starting with B

v. 1.7
date: 2005/04/15 18:48:56;  author: leeym;  state: Exp;  lines: +11 -8
- update grappa to 2.0
- utilize PLIST_FILES
- unbreak it on 4.x
- update maintainer's email

PR:		79241
Submitted by:	David A. Bader 

v. 1.6
date: 2004/08/17 10:29:40;  author: kris;  state: Exp;  lines: +1 -7
This is now buildable on 5.x, remove BROKEN.

v. 1.5
date: 2004/02/04 05:18:50;  author: marcus;  state: Exp;  lines: +1 -0
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)

v. 1.4
date: 2003/12/19 10:22:05;  author: linimon;  state: Exp;  lines: +7 -1
Mark as broken on 5.x due to the usual gcc terminating-character hassles.
Notified mainatainer.

v. 1.3
date: 2003/02/21 11:01:34;  author: knu;  state: Exp;  lines: +2 -1
De-pkg-comment.

v. 1.2
date: 2001/08/29 11:53:29;  author: wjv;  state: Exp;  lines: +3 -3
- Update to version 1.0.3

PR:		30175
Submitted by:	David A. Bader  (MAINTAINER)

v. 1.1
date: 2001/07/04 08:39:35;  author: wjv;  state: Exp;
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny
Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu
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