# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	/usr/ports/biology/treepuzzle
#	/usr/ports/biology/treepuzzle/Makefile
#	/usr/ports/biology/treepuzzle/pkg-comment
#	/usr/ports/biology/treepuzzle/distinfo
#	/usr/ports/biology/treepuzzle/pkg-descr
#	/usr/ports/biology/treepuzzle/pkg-plist
#
echo c - /usr/ports/biology/treepuzzle
mkdir -p /usr/ports/biology/treepuzzle > /dev/null 2>&1
echo x - /usr/ports/biology/treepuzzle/Makefile
sed 's/^X//' >/usr/ports/biology/treepuzzle/Makefile << 'END-of-/usr/ports/biology/treepuzzle/Makefile'
X# Ports collection makefile for:	treepuzzle
X# Date created:				26 August 2002
X# Whom:					lentferj
X#
X# $FreeBSD$
X#
X
XPORTNAME=	treepuzzle
XPORTVERSION=	5.1
XCATEGORIES=	biology
XMASTER_SITES=	http://www.tree-puzzle.de/
XDISTNAME=	tree-puzzle-${PORTVERSION}
X
XMAINTAINER=	jan.lentfer@web.de
X
XUSE_GMAKE=	yes
XGNU_CONFIGURE=	yes
X
Xdo-install:
X	${INSTALL_PROGRAM} ${WRKSRC}/src/puzzle ${PREFIX}/bin/puzzle
X
X.include <bsd.port.mk>
END-of-/usr/ports/biology/treepuzzle/Makefile
echo x - /usr/ports/biology/treepuzzle/pkg-comment
sed 's/^X//' >/usr/ports/biology/treepuzzle/pkg-comment << 'END-of-/usr/ports/biology/treepuzzle/pkg-comment'
XMaximum likelihood phylogeny reconstruction using quartets
END-of-/usr/ports/biology/treepuzzle/pkg-comment
echo x - /usr/ports/biology/treepuzzle/distinfo
sed 's/^X//' >/usr/ports/biology/treepuzzle/distinfo << 'END-of-/usr/ports/biology/treepuzzle/distinfo'
XMD5 (tree-puzzle-5.1.tar.gz) = 5c33d8c0d2c5da21f246e9bf6a0c3513
END-of-/usr/ports/biology/treepuzzle/distinfo
echo x - /usr/ports/biology/treepuzzle/pkg-descr
sed 's/^X//' >/usr/ports/biology/treepuzzle/pkg-descr << 'END-of-/usr/ports/biology/treepuzzle/pkg-descr'
XTREE-PUZZLE is a computer program to reconstruct phylogenetic trees from
Xmolecular sequence data by maximum likelihood. It implements a fast tree search
Xalgorithm, quartet puzzling, that allows analysis of large data sets and
Xautomatically assigns estimations of support to each internal branch.
XTREE-PUZZLE also computes pairwise maximum likelihood distances as well as
Xbranch lengths for user specified trees. Branch lengths can be calculated under
Xthe clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood
Xmapping, to investigate the support of a hypothesized internal branch without
Xcomputing an overall tree and to visualize the phylogenetic content of a
Xsequence alignment. TREE-PUZZLE also conducts a number of statistical tests on
Xthe data set (chi-square test for homogeneity of base composition, likelihood
Xratio clock test, Kishino-Hasegawa test). The models of substitution provided by
XTREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT,
XWAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity
Xis modeled by a discrete Gamma distribution and by allowing invariable sites.
XThe corresponding parameters can be inferred from the data set.
X
XWWW: http://www.tree-puzzle.de
END-of-/usr/ports/biology/treepuzzle/pkg-descr
echo x - /usr/ports/biology/treepuzzle/pkg-plist
sed 's/^X//' >/usr/ports/biology/treepuzzle/pkg-plist << 'END-of-/usr/ports/biology/treepuzzle/pkg-plist'
Xbin/puzzle
END-of-/usr/ports/biology/treepuzzle/pkg-plist
exit