From 1bc69d7e0ce9117fb4a800b3ffbcb6de72ee189a Mon Sep 17 00:00:00 2001 From: "James E. Housley" Date: Thu, 12 Oct 2000 12:31:13 +0000 Subject: Initial import of fastDNAml Version 1.2.2 The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki --- biology/Makefile | 1 + biology/fastdnaml/Makefile | 30 ++++++++++++++++++++++++++++++ biology/fastdnaml/distinfo | 1 + biology/fastdnaml/pkg-comment | 1 + biology/fastdnaml/pkg-descr | 22 ++++++++++++++++++++++ biology/fastdnaml/pkg-plist | 38 ++++++++++++++++++++++++++++++++++++++ 6 files changed, 93 insertions(+) create mode 100644 biology/fastdnaml/Makefile create mode 100644 biology/fastdnaml/distinfo create mode 100644 biology/fastdnaml/pkg-comment create mode 100644 biology/fastdnaml/pkg-descr create mode 100644 biology/fastdnaml/pkg-plist (limited to 'biology') diff --git a/biology/Makefile b/biology/Makefile index c4b9f79e75f6..b41533083b49 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -7,6 +7,7 @@ SUBDIR += clustalw SUBDIR += deft SUBDIR += emboss + SUBDIR += fastdnaml SUBDIR += gperiodic SUBDIR += hmmer SUBDIR += kinemage diff --git a/biology/fastdnaml/Makefile b/biology/fastdnaml/Makefile new file mode 100644 index 000000000000..203fce448bc6 --- /dev/null +++ b/biology/fastdnaml/Makefile @@ -0,0 +1,30 @@ +# New ports collection makefile for: fastDNAml +# Date created: 12 Oct 2000 +# Whom: Motomichi Matsuzaki +# +# $FreeBSD$ +# + +PORTNAME= fastdnaml +PORTVERSION= 1.2.2 +CATEGORIES= biology +MASTER_SITES= http://geta.life.uiuc.edu:80/~gary/programs/fastDNAml/ +DISTNAME= fastDNAml_${PORTVERSION} + +MAINTAINER= mzaki@e-mail.ne.jp + +do-build: + @(cd ${WRKSRC}/source; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin + ${MKDIR} ${PREFIX}/bin/${PORTNAME} + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/* ${PREFIX}/bin/${PORTNAME} + +post-install: +.if !defined(NOPORTDOCS) + ${MKDIR} ${PREFIX}/share/doc/${PORTNAME} + ${INSTALL_MAN} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME} +.endif + +.include diff --git a/biology/fastdnaml/distinfo b/biology/fastdnaml/distinfo new file mode 100644 index 000000000000..2baf1f29f4b8 --- /dev/null +++ b/biology/fastdnaml/distinfo @@ -0,0 +1 @@ +MD5 (fastDNAml_1.2.2.tar.gz) = dd9c737e0f433879500391d0e229f763 diff --git a/biology/fastdnaml/pkg-comment b/biology/fastdnaml/pkg-comment new file mode 100644 index 000000000000..82a9f02fa95f --- /dev/null +++ b/biology/fastdnaml/pkg-comment @@ -0,0 +1 @@ +The faster variant of DNAML, makes phylogenetic trees using maximum likelihood diff --git a/biology/fastdnaml/pkg-descr b/biology/fastdnaml/pkg-descr new file mode 100644 index 000000000000..391df7e37c84 --- /dev/null +++ b/biology/fastdnaml/pkg-descr @@ -0,0 +1,22 @@ +fastDNAml is a program for estimating maximum likelihood phylogenetic trees +from nucleotide sequences. + +WWW: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html + +fastDNAml is an attempt to solve the same problem as Joseph Felsenstein's +DNAML, but to do so faster and using less memory, so that larger trees and/or +more bootstrap replicates become tractable. Much of fastDNAml is merely a +recoding of the PHYLIP 3.3 DNAML program from PASCAL to C. + +For Felsenstein's phylogenetic analysis softwares, including the latest +versions of DNAML, visit the PHYLIP Home Page: + http://evolution.genetics.washington.edu/phylip.html + +When publishing work that based on results from fastDNAml please cite: + + Felsenstein, J. 1981. Evolutionary trees from DNA sequences: + A maximum likelihood approach. J. Mol. Evol. 17: 368-376. + + Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. + fastDNAml: A tool for construction of phylogenetic trees of DNA + sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48. diff --git a/biology/fastdnaml/pkg-plist b/biology/fastdnaml/pkg-plist new file mode 100644 index 000000000000..d2d7d1f04e57 --- /dev/null +++ b/biology/fastdnaml/pkg-plist @@ -0,0 +1,38 @@ +bin/fastDNAml +bin/fastdnaml/ae2dnaml +bin/fastdnaml/bootstrap +bin/fastdnaml/categories +bin/fastdnaml/categories_file +bin/fastdnaml/checkpoint_summary +bin/fastdnaml/clean_checkpoints +bin/fastdnaml/clean_jumbles +bin/fastdnaml/dnaml_progress +bin/fastdnaml/fastDNAml_boot +bin/fastdnaml/fastDNAml_loop +bin/fastdnaml/frequencies +bin/fastdnaml/global +bin/fastdnaml/iterate_rates +bin/fastdnaml/jumble +bin/fastdnaml/min_info +bin/fastdnaml/n_categories +bin/fastdnaml/n_files +bin/fastdnaml/out.PID +bin/fastdnaml/outgroup +bin/fastdnaml/printdata +bin/fastdnaml/quickadd +bin/fastdnaml/restart +bin/fastdnaml/scores +bin/fastdnaml/transition +bin/fastdnaml/treefile +bin/fastdnaml/treefile2prolog +bin/fastdnaml/trees2NEXUS +bin/fastdnaml/trees2prolog +bin/fastdnaml/userlengths +bin/fastdnaml/usertree +bin/fastdnaml/usertrees +bin/fastdnaml/weights +bin/fastdnaml/weights_categories +share/doc/fastdnaml/fastDNAml_doc_1.2.txt +share/doc/fastdnaml/fastDNAml_scripts.txt +@dirrm bin/fastdnaml +@dirrm share/doc/fastdnaml -- cgit v1.2.3