Date: Tue, 12 Nov 2002 16:04:33 +0100 (CET) From: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/45241: New Port - biology/treepuzzle Message-ID: <200211121504.gACF4XbZ033817@neslonek.bio.tu-darmstadt.de>
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>Number: 45241 >Category: ports >Synopsis: New Port - biology/treepuzzle >Confidential: no >Severity: serious >Priority: medium >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Nov 12 07:10:01 PST 2002 >Closed-Date: >Last-Modified: >Originator: Jan Lentfer >Release: FreeBSD 4.7-RC alpha >Organization: >Environment: System: FreeBSD neslonek.bio.tu-darmstadt.de 4.7-RC FreeBSD 4.7-RC #0: Tue Oct 1 21:30:36 CEST 2002 root@neslonek.bio.tu-darmstadt.de:/usr/obj/usr/src/sys/EV56 alpha >Description: TreePuzzle - A Program for Maximum likelihood phylogeny reconstruction using quartets >How-To-Repeat: >Fix: # 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 >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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