Date: Fri, 30 Jul 2004 14:43:55 +0200 (CEST) From: Jan Lentfer <Jan.Lentfer@web.de> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/69799: Update biology/treepuzzle 5.1 -> 5.2 Message-ID: <20040730124355.B80DC61A5@amdahl.bio.tu-darmstadt.de> Resent-Message-ID: <200407301250.i6UCoUWM012290@freefall.freebsd.org>
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>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 <bsd.port.mk> 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:
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