From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Jul 30 12:50:31 2004 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 2A4D916A4CF for ; Fri, 30 Jul 2004 12:50:31 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 0569D43D67 for ; Fri, 30 Jul 2004 12:50:31 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i6UCoUrO012291 for ; Fri, 30 Jul 2004 12:50:30 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i6UCoUWM012290; Fri, 30 Jul 2004 12:50:30 GMT (envelope-from gnats) Resent-Date: Fri, 30 Jul 2004 12:50:30 GMT Resent-Message-Id: <200407301250.i6UCoUWM012290@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Jan Lentfer Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 4785816A4CE for ; Fri, 30 Jul 2004 12:44:12 +0000 (GMT) Received: from mailserver1.hrz.tu-darmstadt.de (lnx131.hrz.tu-darmstadt.de [130.83.126.63]) by mx1.FreeBSD.org (Postfix) with ESMTP id 1843743D46 for ; Fri, 30 Jul 2004 12:44:11 +0000 (GMT) (envelope-from root@amdahl.bio.tu-darmstadt.de) Received: from amdahl.bio.tu-darmstadt.de (amdahl.bio.tu-darmstadt.de [130.83.207.157])i6UChuSR005038 for ; Fri, 30 Jul 2004 14:43:56 +0200 Received: from localhost (localhost [127.0.0.1]) by amdahl.bio.tu-darmstadt.de (Postfix) with ESMTP id 327D661AB for ; Fri, 30 Jul 2004 14:44:01 +0200 (CEST) Received: from amdahl.bio.tu-darmstadt.de ([127.0.0.1])port 10024) with ESMTP id 35918-02 for ; Fri, 30 Jul 2004 14:43:56 +0200 (CEST) Received: by amdahl.bio.tu-darmstadt.de (Postfix, from userid 0) id B80DC61A5; Fri, 30 Jul 2004 14:43:55 +0200 (CEST) Message-Id: <20040730124355.B80DC61A5@amdahl.bio.tu-darmstadt.de> Date: Fri, 30 Jul 2004 14:43:55 +0200 (CEST) From: Jan Lentfer To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/69799: Update biology/treepuzzle 5.1 -> 5.2 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: Jan Lentfer List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 30 Jul 2004 12:50:31 -0000 >Number: 69799 >Category: ports >Synopsis: Update biology/treepuzzle 5.1 -> 5.2 >Confidential: no >Severity: serious >Priority: high >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Jul 30 12:50:30 GMT 2004 >Closed-Date: >Last-Modified: >Originator: Jan Lentfer >Release: FreeBSD 5.2-CURRENT i386 >Organization: >Environment: System: FreeBSD amdahl.bio.tu-darmstadt.de 5.2-CURRENT FreeBSD 5.2-CURRENT #1: Tue Jul 27 15:26:17 CEST 2004 root@amdahl.bio.tu-darmstadt.de:/usr/src/sys/i386/compile/PPRO_SMP i386 >Description: An error was found in tree-puzzle 5.1 that couls lead to badly resolved trees. 5.1 shouldn't be used anymore.^ >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: # # biology/treepuzzle # biology/treepuzzle/pkg-message # biology/treepuzzle/Makefile # biology/treepuzzle/distinfo # biology/treepuzzle/pkg-descr # echo c - biology/treepuzzle mkdir -p biology/treepuzzle > /dev/null 2>&1 echo x - biology/treepuzzle/pkg-message sed 's/^X//' >biology/treepuzzle/pkg-message << 'END-of-biology/treepuzzle/pkg-message' X--------------------------------------------- X XIf you want to install the parallel version Xof tree-puzzle, you need to install from the Xports and have to have a MPI-Implementation Xon your system. XThe tree-puzzle configure script will Xthen automatically build the normal Xand parallel version (puzzle & ppuzzle). X X--------------------------------------------- END-of-biology/treepuzzle/pkg-message echo x - biology/treepuzzle/Makefile sed 's/^X//' >biology/treepuzzle/Makefile << 'END-of-biology/treepuzzle/Makefile' X# Ports collection makefile for: treepuzzle X# Date created: 26 August 2002 X# Whom: lentferj X# X# $FreeBSD: ports/biology/treepuzzle/Makefile,v 1.3 2004/02/06 13:10:56 trevor Exp $ X# X XPORTNAME= treepuzzle XPORTVERSION= 5.2 XCATEGORIES= biology XMASTER_SITES= http://www.tree-puzzle.de/ XDISTNAME= tree-puzzle-${PORTVERSION} X XMAINTAINER= jan.lentfer@web.de XCOMMENT= Maximum likelihood phylogeny reconstruction using quartets X XGNU_CONFIGURE= yes XCONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL} XPLIST_FILES= bin/puzzle X Xpre-configure: X @${CAT} pkg-message X X.include END-of-biology/treepuzzle/Makefile echo x - biology/treepuzzle/distinfo sed 's/^X//' >biology/treepuzzle/distinfo << 'END-of-biology/treepuzzle/distinfo' XMD5 (tree-puzzle-5.2.tar.gz) = 20fa9606434ddc789670e681d98fe68f XSIZE (tree-puzzle-5.2.tar.gz) = 875142 END-of-biology/treepuzzle/distinfo echo x - biology/treepuzzle/pkg-descr sed 's/^X//' >biology/treepuzzle/pkg-descr << 'END-of-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-biology/treepuzzle/pkg-descr exit >Release-Note: >Audit-Trail: >Unformatted: