treepuzzle 5.2 biology =1

Maximum likelihood phylogeny reconstruction using quartets
Maintained by: jan.lentfer@web.de
Port Added: 20 Nov 2002 09:04:07
License: not specified in port

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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.

WWW: http://www.tree-puzzle.de

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMonThere are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/treepuzzle/ && make install clean
To add the package: pkg_add -r treepuzzle

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Configuration Options

     No options to configure

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Master Sites:

http://www.tree-puzzle.de/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Get Rid MD5 support

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

SHA256ify

Approved by:    krion@

At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE.

Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.

- Update to 5.2

PR:             ports/69799
Submitted by:   Jan Lentfer <Jan.Lentfer@web.de> (maintainer)

SIZEify (maintainer timeout)

Use PLIST_FILES (bento-tested, marcus-reviewed).

De-pkg-comment.

add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets

PR:             45241
Submitted by:   Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>

12 vulnerabilities affecting 17 ports have been reported in the past 14 days

^* - modified, not new

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