From owner-freebsd-ports Thu Oct 12 5:20:11 2000 Delivered-To: freebsd-ports@freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id 80EB237B66E for ; Thu, 12 Oct 2000 05:20:01 -0700 (PDT) Received: (from gnats@localhost) by freefall.freebsd.org (8.9.3/8.9.2) id FAA78247; Thu, 12 Oct 2000 05:20:01 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: by hub.freebsd.org (Postfix, from userid 32767) id 3E2A637B502; Thu, 12 Oct 2000 05:18:24 -0700 (PDT) Message-Id: <20001012121824.3E2A637B502@hub.freebsd.org> Date: Thu, 12 Oct 2000 05:18:24 -0700 (PDT) From: mzaki@e-mail.ne.jp To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-1.0 Subject: ports/21931: New port: fastDNAml: famous molecular biology tool Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk X-Loop: FreeBSD.org >Number: 21931 >Category: ports >Synopsis: New port: fastDNAml: famous molecular biology tool >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Oct 12 05:20:01 PDT 2000 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: current >Organization: >Environment: >Description: fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. This is a famous tool for molecular biology . >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: # # biol/fastdnaml # biol/fastdnaml/Makefile # biol/fastdnaml/distinfo # biol/fastdnaml/pkg-comment # biol/fastdnaml/pkg-descr # biol/fastdnaml/pkg-plist # echo c - biol/fastdnaml mkdir -p biol/fastdnaml > /dev/null 2>&1 echo x - biol/fastdnaml/Makefile sed 's/^X//' >biol/fastdnaml/Makefile << 'END-of-biol/fastdnaml/Makefile' X# New ports collection makefile for: fastDNAml X# Date created: 12 Oct 2000 X# Whom: Motomichi Matsuzaki X# X# $FreeBSD$ X# X XPORTNAME= fastdnaml XPORTVERSION= 1.2.2 XCATEGORIES= biology XMASTER_SITES= http://geta.life.uiuc.edu:80/~gary/programs/fastDNAml/ XDISTNAME= fastDNAml_${PORTVERSION} X XMAINTAINER= mzaki@e-mail.ne.jp X Xdo-build: X @(cd ${WRKSRC}/source; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) X Xdo-install: X ${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin X ${MKDIR} ${PREFIX}/bin/${PORTNAME} X ${INSTALL_SCRIPT} ${WRKSRC}/scripts/* ${PREFIX}/bin/${PORTNAME} X Xpost-install: X.if !defined(NOPORTDOCS) X ${MKDIR} ${PREFIX}/share/doc/${PORTNAME} X ${INSTALL_MAN} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME} X.endif X X.include END-of-biol/fastdnaml/Makefile echo x - biol/fastdnaml/distinfo sed 's/^X//' >biol/fastdnaml/distinfo << 'END-of-biol/fastdnaml/distinfo' XMD5 (fastDNAml_1.2.2.tar.gz) = dd9c737e0f433879500391d0e229f763 END-of-biol/fastdnaml/distinfo echo x - biol/fastdnaml/pkg-comment sed 's/^X//' >biol/fastdnaml/pkg-comment << 'END-of-biol/fastdnaml/pkg-comment' XThe faster variant of DNAML, makes phylogenetic trees using maximum likelihood END-of-biol/fastdnaml/pkg-comment echo x - biol/fastdnaml/pkg-descr sed 's/^X//' >biol/fastdnaml/pkg-descr << 'END-of-biol/fastdnaml/pkg-descr' XfastDNAml is a program for estimating maximum likelihood phylogenetic trees Xfrom nucleotide sequences. X XWWW: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html X XfastDNAml is an attempt to solve the same problem as Joseph Felsenstein's XDNAML, but to do so faster and using less memory, so that larger trees and/or Xmore bootstrap replicates become tractable. Much of fastDNAml is merely a Xrecoding of the PHYLIP 3.3 DNAML program from PASCAL to C. X XFor Felsenstein's phylogenetic analysis softwares, including the latest Xversions of DNAML, visit the PHYLIP Home Page: X http://evolution.genetics.washington.edu/phylip.html X XWhen publishing work that based on results from fastDNAml please cite: X X Felsenstein, J. 1981. Evolutionary trees from DNA sequences: X A maximum likelihood approach. J. Mol. Evol. 17: 368-376. X X Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. X fastDNAml: A tool for construction of phylogenetic trees of DNA X sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48. END-of-biol/fastdnaml/pkg-descr echo x - biol/fastdnaml/pkg-plist sed 's/^X//' >biol/fastdnaml/pkg-plist << 'END-of-biol/fastdnaml/pkg-plist' Xbin/fastDNAml Xbin/fastdnaml/ae2dnaml Xbin/fastdnaml/bootstrap Xbin/fastdnaml/categories Xbin/fastdnaml/categories_file Xbin/fastdnaml/checkpoint_summary Xbin/fastdnaml/clean_checkpoints Xbin/fastdnaml/clean_jumbles Xbin/fastdnaml/dnaml_progress Xbin/fastdnaml/fastDNAml_boot Xbin/fastdnaml/fastDNAml_loop Xbin/fastdnaml/frequencies Xbin/fastdnaml/global Xbin/fastdnaml/iterate_rates Xbin/fastdnaml/jumble Xbin/fastdnaml/min_info Xbin/fastdnaml/n_categories Xbin/fastdnaml/n_files Xbin/fastdnaml/out.PID Xbin/fastdnaml/outgroup Xbin/fastdnaml/printdata Xbin/fastdnaml/quickadd Xbin/fastdnaml/restart Xbin/fastdnaml/scores Xbin/fastdnaml/transition Xbin/fastdnaml/treefile Xbin/fastdnaml/treefile2prolog Xbin/fastdnaml/trees2NEXUS Xbin/fastdnaml/trees2prolog Xbin/fastdnaml/userlengths Xbin/fastdnaml/usertree Xbin/fastdnaml/usertrees Xbin/fastdnaml/weights Xbin/fastdnaml/weights_categories Xshare/doc/fastdnaml/fastDNAml_doc_1.2.txt Xshare/doc/fastdnaml/fastDNAml_scripts.txt X@dirrm bin/fastdnaml X@dirrm share/doc/fastdnaml END-of-biol/fastdnaml/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