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>
The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.
Citation:
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.
The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.
WWW: http://www.drive5.com/muscle/
PR: ports/118460
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
The xorp port will now log to /var/log/xorp_rtrmgr.log by default, and
the xorp_rtrmgr process will be run under daemon(8) to detach it from
the controlling terminal.
kqemu only accellerates qemu-system-x86_64 on amd64 that were missing
in qemu's pkg-message [1]
- Update the note about kqemu on amd64 SMP, and add a reminder to keep
kqemu in sync with the kernel while I'm at it
- Bump PORTREVISION
Noticed by: bakul [1]
Updated for a FreeBSD 7.0 and above byte level locking
change. The problem was reported by Conrad J. Sabatier
<conrads@cox.net>, who helped test the update. Wesley
Shields <wxs@FreeBSD.org> provided an 8.0-CURRENT test
system.
Propagated the FreeBSD 7.0 and above locking changes to
FreeBSD 6.x, based on a report from Edwin Groothuis
<edwin@FreeBSD.org>.
(as a note about the above, if the port still fails for you, you should upgrade
your system either to the latest HEAD or the latest 7-STALBE there's a 2 weeks
window of breakage or so).
Added warnings for unsupported dialects or versions.
Added a missing quote to the Configure script's
FreeBSD stanza.
PR: ports/123615
Submitted by: maintainer
Supplimentary tindy testing by: miwi@
