notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
Port details
njplot Phylogenetic tree drawing program
2.4 biology Deleted 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 View this port on Repology. pkg-fallout 2.4Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2008-05-14 14:07:25
Last Update: 2018-12-11 15:04:12
SVN Revision: 487239
People watching this port, also watch:: tmux, font-misc-meltho, xclock, p5-Net-HTTP
License: NONE
WWW:
http://pbil.univ-lyon1.fr/software/njplot.html
Description:
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
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
pkg-plist: as obtained via: make generate-plist
Expand this list (9 items)
Collapse this list.
  1. bin/newicktops
  2. bin/newicktotxt
  3. bin/njplot
  4. bin/unrooted
  5. man/man1/njplot.1.gz
  6. man/man1/unrooted.1.gz
  7. /usr/local/share/licenses/njplot-2.4/catalog.mk
  8. /usr/local/share/licenses/njplot-2.4/LICENSE
  9. /usr/local/share/licenses/njplot-2.4/NONE
Collapse this list.
Dependency lines:
  • njplot>0:biology/njplot
No installation instructions:
This port has been deleted.
PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1479168824 SHA256 (njplot-2.4.tar.gz) = e470f7583691da2ad36a7cda4269bf64807f77cb27fe1e16cbfefc45942469d3 SIZE (njplot-2.4.tar.gz) = 83239

No package information for this port in our database
Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link: pkg-fallout
Dependencies
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
Options name:
N/A
USES:
motif
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (3 items)
Collapse this list.
  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/
Collapse this list.

Number of commits found: 19

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.4
11 Dec 2018 15:04:12
Revision:487239Original commit files touched by this commit
jrm search for other commits by this committer
Remove biology/njplot

The author of both NJplot and SeaView says that NJplot can be considered
deprecated and replaced by SeaView.
2.4
28 Nov 2016 15:19:42
Revision:427329Original commit files touched by this commit
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
2.4
16 Nov 2016 14:52:53
Revision:426241Original commit files touched by this commit
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
2.1_3
28 Nov 2015 23:08:03
Revision:402562Original commit files touched by this commit
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)
2.1_3
25 Oct 2015 19:35:28
Revision:400160Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
2.1_3
05 Apr 2015 17:55:36
Revision:383309Original commit files touched by this commit
bapt search for other commits by this committer
Mark as broken unfetchable ports
2.1_3
01 Jun 2014 11:26:39
Revision:356098Original commit files touched by this commit
ohauer search for other commits by this committer
- add stage support
- add OPTION for X11
- bump PORTREVISION
2.1_2
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
2.1_2
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
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)
2.1_2
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
2.1_2
22 Sep 2013 18:05:05
Revision:327888Original commit files touched by this commit
bapt search for other commits by this committer
Fix NO_STAGE attribution
2.1_2
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
2.1_2
10 Jul 2013 07:33:24
Revision:322624Original commit files touched by this commit
bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
2.1_2
24 Jun 2012 21:53:38
Original commit files touched by this commit
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.
2.1_2
02 May 2011 12:44:53
Original commit files touched by this commit
makc search for other commits by this committer
Bump PORTREVISION after open-mofit update
2.1_1
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
2.1_1
09 Jun 2009 15:33:28
Original commit files touched by this commit
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)
2.1
17 May 2008 16:52:34
Original commit files touched by this commit
pav search for other commits by this committer
- Update maintainer's email address

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
2.1
14 May 2008 14:07:01
Original commit files touched by this commit
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: 19