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 <mzaki@e-mail.ne.jp>

biology/Makefile

@@ -7,6 +7,7 @@
     SUBDIR += clustalw
     SUBDIR += deft
     SUBDIR += emboss
+    SUBDIR += fastdnaml
     SUBDIR += gperiodic
     SUBDIR += hmmer
     SUBDIR += kinemage

biology/fastdnaml/Makefile

@@ -0,0 +1,30 @@
+# New ports collection makefile for:	fastDNAml
+# Date created:		12 Oct 2000
+# Whom:	      		Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
+#
+# $FreeBSD$
+#
+
+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 <bsd.port.mk>

biology/fastdnaml/distinfo

@@ -0,0 +1 @@
+MD5 (fastDNAml_1.2.2.tar.gz) = dd9c737e0f433879500391d0e229f763

biology/fastdnaml/pkg-comment

@@ -0,0 +1 @@
+The faster variant of DNAML, makes phylogenetic trees using maximum likelihood

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.

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