| Port details |
- treepuzzle Maximum likelihood phylogeny reconstruction using quartets
- 5.2 biology
 =0      5.2Version of this port present on the latest quarterly branch. - Maintainer: jan.lentfer@web.de
- Port Added: 2002-11-20 09:04:07
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- License: not specified in port
- WWW:
- http://www.tree-puzzle.de
- Description:
- TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from
molecular sequence data by maximum likelihood. It implements a fast tree search
algorithm, quartet puzzling, that allows analysis of large data sets and
automatically assigns estimations of support to each internal branch.
TREE-PUZZLE also computes pairwise maximum likelihood distances as well as
branch lengths for user specified trees. Branch lengths can be calculated under
the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood
mapping, to investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of a
sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on
the data set (chi-square test for homogeneity of base composition, likelihood
ratio clock test, Kishino-Hasegawa test). The models of substitution provided by
TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT,
WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity
is modeled by a discrete Gamma distribution and by allowing invariable sites.
The corresponding parameters can be inferred from the data set.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- treepuzzle>0:biology/treepuzzle
- To install the port:
- cd /usr/ports/biology/treepuzzle/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/treepuzzle
- pkg install treepuzzle
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: treepuzzle
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (tree-puzzle-5.2.tar.gz) = 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb
SIZE (tree-puzzle-5.2.tar.gz) = 875142
Packages (timestamps in pop-ups are UTC):
- This port has no dependencies.
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_treepuzzle
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 16
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
07 Sep 2022 21:58:51
 |
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
5.2
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
5.2
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
5.2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
5.2
25 Sep 2013 00:54:09
 |
bdrewery |
- Remove NO_STAGE as these have been tested to be safe
With hat: portmgr |
5.2
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
5.2
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
5.2
21 Aug 2008 06:18:49
|
rafan |
Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk (Only the first 15 lines of the commit message are shown above ) |
5.2
22 Jan 2006 08:20:34
|
edwin |
SHA256ify
Approved by: krion@ |
5.2
12 Apr 2005 03:26:57
|
obrien |
At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE. |
5.2
11 Apr 2005 08:04:41
|
obrien |
Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'. |
5.2
30 Jul 2004 22:02:00
|
pav |
- Update to 5.2
PR: ports/69799
Submitted by: Jan Lentfer <Jan.Lentfer@web.de> (maintainer) |
5.1
31 Mar 2004 03:12:58
|
trevor |
SIZEify (maintainer timeout) |
5.1
06 Feb 2004 13:12:53
|
trevor |
Use PLIST_FILES (bento-tested, marcus-reviewed). |
5.1
21 Feb 2003 11:01:38
|
knu |
De-pkg-comment. |
5.1
20 Nov 2002 08:54:11
|
ijliao |
add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets
PR: 45241
Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de> |
Number of commits found: 16
|
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