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