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Port details
njplot Phylogenetic tree drawing program
2.4 biology on this many watch lists=1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 14 May 2008 14:07:25
License: NONE
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
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/njplot/ && make install clean
To add the package: pkg install njplot

PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles

distinfo:

TIMESTAMP = 1479168824
SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3
SIZE (njplot-2.4.tar.gz) = 83239


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. blastall : biology/ncbi-toolkit
  2. x11.pc : x11/libX11
  3. xmu.pc : x11-toolkits/libXmu
  4. xp.pc : x11/libXp
  5. xt.pc : x11-toolkits/libXt
  6. xpm.pc : x11/libXpm
Runtime dependencies:
  1. x11.pc : x11/libX11
  2. xmu.pc : x11-toolkits/libXmu
  3. xp.pc : x11/libXp
  4. xt.pc : x11-toolkits/libXt
  5. xpm.pc : x11/libXpm
Library dependencies:
  1. libXm.so.4 : x11-toolkits/open-motif
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for njplot-2.4:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
motif

Master Sites:
  1. ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/
  2. ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/
  3. http://awarnach.mathstat.dal.ca/distfiles/

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
28 Nov 2016 15:19:42
Original commit files touched by this commit  2.4
Revision:427329
jrm search for other commits by this committer
biology/njplot: Add site in MASTER_SITES because package builders are
timing out during fetch.

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D8651
16 Nov 2016 14:52:53
Original commit files touched by this commit  2.4
Revision:426241
jrm search for other commits by this committer
biology/njplot: Revive and update to version 2.4

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D8518
28 Nov 2015 23:08:03
Original commit files touched by this commit  2.1_3
Revision:402562
rene search for other commits by this committer
Remove expired ports:
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by
upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
2015-11-26 databases/sybtcl: Broken for more than 6 months
2015-11-26 biology/povchem: Broken for more than 6 months
2015-11-26 audio/btc: Broken for more than 6 months
2015-11-26 astro/wmglobe: Broken for more than 6 months
2015-11-26 graphics/pyro: Broken for more than 6 months
2015-11-26 graphics/jpeg2ps: Broken for more than 6 months
2015-11-26 chinese/gugod-clean: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
25 Oct 2015 19:35:28
Original commit files touched by this commit  2.1_3
Revision:400160
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
05 Apr 2015 17:55:36
Original commit files touched by this commit  2.1_3
Revision:383309
bapt search for other commits by this committer
Mark as broken unfetchable ports
01 Jun 2014 11:26:39
Original commit files touched by this commit  2.1_3
Revision:356098
ohauer search for other commits by this committer
- add stage support
- add OPTION for X11
- bump PORTREVISION
21 Feb 2014 13:35:26
Original commit files touched by this commit  2.1_2
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  2.1_2
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  2.1_2
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
22 Sep 2013 18:05:05
Original commit files touched by this commit  2.1_2
Revision:327888
bapt search for other commits by this committer
Fix NO_STAGE attribution
20 Sep 2013 15:55:44
Original commit files touched by this commit  2.1_2
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
10 Jul 2013 07:33:24
Original commit files touched by this commit  2.1_2
Revision:322624
bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
24 Jun 2012 21:53:38
Original commit files touched by this commit  2.1_2
dougb search for other commits by this committer
s/X11BASE/LOCALBASE/, or equivalent.

The X11BASE variable is long gone, however these ports were not updated.
02 May 2011 12:44:53
Original commit files touched by this commit  2.1_2
makc search for other commits by this committer
Bump PORTREVISION after open-mofit update
19 Mar 2011 12:38:54
Original commit files touched by this commit  2.1_1
miwi search for other commits by this committer
- Get Rid MD5 support
09 Jun 2009 15:33:28
Original commit files touched by this commit  2.1_1
amdmi3 search for other commits by this committer
Convert most of remaining ports that depend on xorg-libraries to
modular xorg.

- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
  above change
- a few minor nits like whitespace and SF macro

Tested by:      2 tinderbox runs by pav
Approved by:    portmgr (pav)
17 May 2008 16:52:34
Original commit files touched by this commit  2.1
pav search for other commits by this committer
- Update maintainer's email address

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
14 May 2008 14:07:01
Original commit files touched by this commit  2.1
pav search for other commits by this committer
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>

Number of commits found: 18

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