Bug 118438

Summary: New port: biology/njplot Phylogenetic tree drawing program
Product: Ports & Packages Reporter: Motomichi Matsuzaki <mzaki>
Component: Individual Port(s)Assignee: freebsd-ports-bugs (Nobody) <ports-bugs>
Status: Closed FIXED    
Severity: Affects Only Me    
Priority: Normal    
Version: Latest   
Hardware: Any   
OS: Any   
Attachments:
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Description Motomichi Matsuzaki 2007-12-05 04:50:00 UTC 
NJplot is a tree drawing program able to draw any phylogenetic tree expressed
in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.

WWW: http://pbil.univ-lyon1.fr/software/njplot.html

Although there are no explicit licensing statements fot NJplot,
the submitter has confirmed by e-mail to the author
that it can be redistributed in source and in binary forms without restrictions.

The package contains 4 programs: njplot, newicktops, newicktotxt, unrooted.
If -DWITHOUT_X11 is specified, 2 non-interactive programs (newickto{ps,txt})
will be built.

Fix: Patch attached with submission follows:
Comment 1 Pav Lucistnik freebsd_committer freebsd_triage 2008-05-14 14:53:41 UTC 
State Changed
From-To: open->closed

New port added, thanks! 

I have switched to the versioned distfile in archive/ subdir.
Comment 2 dfilter service freebsd_committer freebsd_triage 2008-05-14 15:07:08 UTC 
pav         2008-05-14 14:07:01 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/njplot       Makefile distinfo pkg-descr 
    biology/njplot/files patch-makefile 
  Log:
  NJplot is a tree drawing program able to draw any phylogenetic tree expressed
  in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
  package). NJplot is especially convenient for rooting the unrooted trees
  obtained from parsimony, distance or maximum likelihood tree-building methods.
  
  The package contains the following programs:
  njplot      - draw phylogenetic trees and interactively modify them
  newicktops  - non-interactive version rendering into a PostScript file
  newicktotxt - non-interactive version rendering into a text file
  unrooted    - draw unrooted circular trees
  
  If you use NJplot in a published work, please cite the following reference:
  
  Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
  biological sequence banks. Biochimie, 78, 364-369.
  
  WWW: http://pbil.univ-lyon1.fr/software/njplot.html
  
  PR:             ports/118438
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.97      +1 -0      ports/biology/Makefile
  1.1       +55 -0     ports/biology/njplot/Makefile (new)
  1.1       +3 -0      ports/biology/njplot/distinfo (new)
  1.1       +69 -0     ports/biology/njplot/files/patch-makefile (new)
  1.1       +17 -0     ports/biology/njplot/pkg-descr (new)
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