From owner-freebsd-ports Tue Nov 12 7:10: 9 2002 Delivered-To: freebsd-ports@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 59ED337B404 for ; Tue, 12 Nov 2002 07:10:05 -0800 (PST) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 854D343E6E for ; Tue, 12 Nov 2002 07:10:02 -0800 (PST) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.12.6/8.12.6) with ESMTP id gACFA2x3056249 for ; Tue, 12 Nov 2002 07:10:02 -0800 (PST) (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.6/8.12.6/Submit) id gACFA2H6056248; Tue, 12 Nov 2002 07:10:02 -0800 (PST) Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 351D737B401 for ; Tue, 12 Nov 2002 07:06:28 -0800 (PST) Received: from neslonek.bio.tu-darmstadt.de (neslonek.bio.tu-darmstadt.de [130.83.207.147]) by mx1.FreeBSD.org (Postfix) with ESMTP id 5CE8643E4A for ; Tue, 12 Nov 2002 07:06:26 -0800 (PST) (envelope-from lentferj@neslonek.bio.tu-darmstadt.de) Received: from neslonek.bio.tu-darmstadt.de (localhost.bio.tu-darmstadt.de [127.0.0.1]) by neslonek.bio.tu-darmstadt.de (8.12.3/8.12.3) with ESMTP id gACF4ZbH033818 for ; Tue, 12 Nov 2002 16:04:36 +0100 (CET) (envelope-from lentferj@neslonek.bio.tu-darmstadt.de) Received: (from root@localhost) by neslonek.bio.tu-darmstadt.de (8.12.3/8.12.3/Submit) id gACF4XbZ033817; Tue, 12 Nov 2002 16:04:33 +0100 (CET) Message-Id: <200211121504.gACF4XbZ033817@neslonek.bio.tu-darmstadt.de> Date: Tue, 12 Nov 2002 16:04:33 +0100 (CET) From: Jan Lentfer Reply-To: Jan Lentfer To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/45241: New Port - biology/treepuzzle Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >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 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