add treepuzzle 5.1

Maximum likelihood phylogeny reconstruction using quartets

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

biology/Makefile

@@ -56,6 +56,7 @@
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker
+    SUBDIR += treepuzzle
     SUBDIR += treeviewx
     SUBDIR += wise
     SUBDIR += xdrawchem

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>

biology/treepuzzle/distinfo

@@ -0,0 +1 @@
+MD5 (tree-puzzle-5.1.tar.gz) = 5c33d8c0d2c5da21f246e9bf6a0c3513

biology/treepuzzle/pkg-comment

@@ -0,0 +1 @@
+Maximum likelihood phylogeny reconstruction using quartets

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

biology/treepuzzle/pkg-plist

@@ -0,0 +1 @@
+bin/puzzle