Import of fastDNAml-1.2.1, a program for estimating maximum likelihood

phylogenetic trees from nucleotide sequences, as submitted by Marc Baudoin,
thanks!

5 files changed, 83 insertions, 0 deletions

diff --git a/biology/fastDNAml/Makefile b/biology/fastDNAml/Makefile
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+++ b/biology/fastDNAml/Makefile
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+# $NetBSD: Makefile,v 1.1.1.1 1999/07/28 20:18:55 rh Exp $
+
+DISTNAME=	fastDNAml_1.2.1
+PKGNAME=	fastDNAml-1.2.1
+WRKSRC=		${WRKDIR}/${DISTNAME}
+CATEGORIES=	biology
+MASTER_SITES=	http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
+
+MAINTAINER=	babafou@babafou.eu.org
+HOMEPAGE=	http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
+
+NO_CDROM=	"No commercial distribution without a royalty agreement with the author"
+
+do-build :
+	@ cd ${WRKSRC}/source && ${MAKE} LDFLAGS=-lm fastDNAml
+
+do-install :
+	${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin
+.for SCRIPT in ae2dnaml bootstrap categories categories_file		\
+		checkpoint_summary clean_checkpoints clean_jumbles	\
+		dnaml_progress fastDNAml_boot fastDNAml_loop		\
+		frequencies global iterate_rates jumble min_info	\
+		n_categories n_files out.PID outgroup printdata		\
+		quickadd restart scores transition treefile		\
+		treefile2prolog trees2NEXUS trees2prolog userlengths	\
+		usertree usertrees weights weights_categories
+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${SCRIPT} ${PREFIX}/bin
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/fastDNAml
+	${INSTALL_DATA} ${WRKSRC}/docs/fastDNAml_doc_1.2.txt ${PREFIX}/share/doc/fastDNAml
+	${INSTALL_DATA} ${WRKSRC}/docs/fastDNAml_scripts.txt ${PREFIX}/share/doc/fastDNAml
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/fastDNAml/files/md5 b/biology/fastDNAml/files/md5
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+++ b/biology/fastDNAml/files/md5
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+$NetBSD: md5,v 1.1.1.1 1999/07/28 20:18:55 rh Exp $
+
+MD5 (fastDNAml_1.2.1.tar.gz) = 61bb05165810ff6813ee13624ab08511
diff --git a/biology/fastDNAml/pkg/COMMENT b/biology/fastDNAml/pkg/COMMENT
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+++ b/biology/fastDNAml/pkg/COMMENT
@@ -0,0 +1 @@
+Program derived from Joseph Felsenstein's version 3.3 DNAML
diff --git a/biology/fastDNAml/pkg/DESCR b/biology/fastDNAml/pkg/DESCR
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+++ b/biology/fastDNAml/pkg/DESCR
@@ -0,0 +1,8 @@
+fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+(part of his PHYLIP package).  Users should consult the documentation for
+DNAML before using this program.
+
+fastDNAml is an attempt to solve the same problem as 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.
diff --git a/biology/fastDNAml/pkg/PLIST b/biology/fastDNAml/pkg/PLIST
new file mode 100644
index 00000000000..dd90ff93ad5
--- /dev/null
+++ b/biology/fastDNAml/pkg/PLIST
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+@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 20:18:56 rh Exp $
+bin/fastDNAml
+bin/ae2dnaml
+bin/bootstrap
+bin/categories
+bin/categories_file
+bin/checkpoint_summary
+bin/clean_checkpoints
+bin/clean_jumbles
+bin/dnaml_progress
+bin/fastDNAml_boot
+bin/fastDNAml_loop
+bin/frequencies
+bin/global
+bin/iterate_rates
+bin/jumble
+bin/min_info
+bin/n_categories
+bin/n_files
+bin/out.PID
+bin/outgroup
+bin/printdata
+bin/quickadd
+bin/restart
+bin/scores
+bin/transition
+bin/treefile
+bin/treefile2prolog
+bin/trees2NEXUS
+bin/trees2prolog
+bin/userlengths
+bin/usertree
+bin/usertrees
+bin/weights
+bin/weights_categories
+share/doc/fastDNAml/fastDNAml_doc_1.2.txt
+share/doc/fastDNAml/fastDNAml_scripts.txt
+@dirrm share/doc/fastDNAml