diff options
| author | Ying-Chieh Liao <ijliao@FreeBSD.org> | 2002-11-20 08:54:10 +0000 |
|---|---|---|
| committer | Ying-Chieh Liao <ijliao@FreeBSD.org> | 2002-11-20 08:54:10 +0000 |
| commit | 545bf7ae46a2555f2dfdc61eda14dd4a36231869 (patch) | |
| tree | a1c5ea293dfb29b99879feae577133ae0d82ea2c /biology | |
| parent | Upgrade to 2.9.26b, fixes bugs in configure script. (diff) | |
add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets
PR: 45241
Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
Notes
Notes:
svn path=/head/; revision=70552
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/treepuzzle/Makefile | 19 | ||||
| -rw-r--r-- | biology/treepuzzle/distinfo | 1 | ||||
| -rw-r--r-- | biology/treepuzzle/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/treepuzzle/pkg-descr | 18 | ||||
| -rw-r--r-- | biology/treepuzzle/pkg-plist | 1 |
6 files changed, 41 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index d11073f74256..9a4012bc0a77 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -56,6 +56,7 @@ SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker + SUBDIR += treepuzzle SUBDIR += treeviewx SUBDIR += wise SUBDIR += xdrawchem diff --git a/biology/treepuzzle/Makefile b/biology/treepuzzle/Makefile new file mode 100644 index 000000000000..5da85ab92905 --- /dev/null +++ b/biology/treepuzzle/Makefile @@ -0,0 +1,19 @@ +# Ports collection makefile for: treepuzzle +# Date created: 26 August 2002 +# Whom: lentferj +# +# $FreeBSD$ +# + +PORTNAME= treepuzzle +PORTVERSION= 5.1 +CATEGORIES= biology +MASTER_SITES= http://www.tree-puzzle.de/ +DISTNAME= tree-puzzle-${PORTVERSION} + +MAINTAINER= jan.lentfer@web.de + +GNU_CONFIGURE= yes +CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL} + +.include <bsd.port.mk> diff --git a/biology/treepuzzle/distinfo b/biology/treepuzzle/distinfo new file mode 100644 index 000000000000..bc21071484fc --- /dev/null +++ b/biology/treepuzzle/distinfo @@ -0,0 +1 @@ +MD5 (tree-puzzle-5.1.tar.gz) = 5c33d8c0d2c5da21f246e9bf6a0c3513 diff --git a/biology/treepuzzle/pkg-comment b/biology/treepuzzle/pkg-comment new file mode 100644 index 000000000000..f74e1b28b924 --- /dev/null +++ b/biology/treepuzzle/pkg-comment @@ -0,0 +1 @@ +Maximum likelihood phylogeny reconstruction using quartets diff --git a/biology/treepuzzle/pkg-descr b/biology/treepuzzle/pkg-descr new file mode 100644 index 000000000000..1e51ea40d926 --- /dev/null +++ b/biology/treepuzzle/pkg-descr @@ -0,0 +1,18 @@ +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 diff --git a/biology/treepuzzle/pkg-plist b/biology/treepuzzle/pkg-plist new file mode 100644 index 000000000000..97facbda9454 --- /dev/null +++ b/biology/treepuzzle/pkg-plist @@ -0,0 +1 @@ +bin/puzzle |