Add paml version 3.01.

A set of utilities for performing Phylogenetic Analysis by Maximum
Likelihood (PAML).

PR:		19753
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>

7 files changed, 89 insertions, 0 deletions

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
new file mode 100644
index 00000000000..5b792993ec0
--- /dev/null
+++ b/biology/paml/Makefile
@@ -0,0 +1,32 @@
+# New ports collection makefile for:	paml
+# Date created:				7 July 2000
+# Whom:					dbader@eece.unm.edu
+#
+# $FreeBSD$
+#
+
+PORTNAME=	paml
+PORTVERSION=	3.01
+CATEGORIES=	biology
+MASTER_SITES=	ftp://abacus.gene.ucl.ac.uk/pub/paml/
+DISTNAME=	paml3.0a
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	dbader@eece.unm.edu
+
+NO_WRKSUBDIR=	yes
+
+BINARIES=	baseml basemlg chi2 codeml codemlsites evolver mcmctree \
+		pamp yn00
+
+do-install:
+.for f in ${BINARIES}
+		${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
+.endfor
+.if !defined(NOPORTDOCS)
+		${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
+		${INSTALL_DATA} ${WRKSRC}/pamlDOC.pdf \
+			${PREFIX}/share/doc/${PORTNAME}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
new file mode 100644
index 00000000000..fd6ef9254a3
--- /dev/null
+++ b/biology/paml/distinfo
@@ -0,0 +1 @@
+MD5 (paml3.0a.tar.Z) = 53ce654a8173407a3db278d106deb115
diff --git a/biology/paml/files/patch-aa b/biology/paml/files/patch-aa
new file mode 100644
index 00000000000..4a5d5b54677
--- /dev/null
+++ b/biology/paml/files/patch-aa
@@ -0,0 +1,11 @@
+--- Makefile.orig	Sun Mar 12 20:49:36 2000
++++ Makefile	Fri Jul  7 06:32:33 2000
+@@ -1,7 +1,7 @@
+ PRGS =  baseml codeml codemlsites basemlg pamp evolver mcmctree yn00 chi2 
+ CC = cc # cc, gcc, cl
+ 
+-CFLAGS = -fast
++CFLAGS += -O3
+ 
+ #CFLAGS = -w0 -warnprotos -newc -std -fast
+ #CFLAGS = -g -w0 -warnprotos -newc -std -edit1 #
diff --git a/biology/paml/files/patch-ab b/biology/paml/files/patch-ab
new file mode 100644
index 00000000000..b0146af8803
--- /dev/null
+++ b/biology/paml/files/patch-ab
@@ -0,0 +1,11 @@
+--- evolver.c-orig	Thu Jun 15 14:42:52 2000
++++ evolver.c	Fri Jul  7 06:40:09 2000
+@@ -63,7 +63,7 @@
+ static double Qfactor=-1, Qrates[5];  /* Qrates[] hold kappa's for nucleotides */
+ 
+ 
+-void main(int argc, char*argv[])
++main(int argc, char*argv[])
+ {
+    char *MCctlf=NULL, outf[]="evolver.out";
+    int i, option=6, ntree=1,rooted, BD=0;
diff --git a/biology/paml/pkg-comment b/biology/paml/pkg-comment
new file mode 100644
index 00000000000..28176e9a1ed
--- /dev/null
+++ b/biology/paml/pkg-comment
@@ -0,0 +1 @@
+Phylogenetic Analysis by Maximum Likelihood (PAML)
diff --git a/biology/paml/pkg-descr b/biology/paml/pkg-descr
new file mode 100644
index 00000000000..e0fa6455430
--- /dev/null
+++ b/biology/paml/pkg-descr
@@ -0,0 +1,22 @@
+Phylogenetic Analysis by Maximum Likelihood (PAML)
+
+PAML is a program package for phylogenetic analyses of DNA or protein
+sequences using maximum likelihood, and is maintained and distributed
+by Ziheng Yang. 
+
+Possible uses of the programs are:
+- Estimation of branch lengths in a phylogenetic tree and parameters
+  in the evolutionary model such as the transition/transversion rate
+  ratio, the shape parameter of the gamma distribution for variable
+  evolutionary rates among sites, and rate parameters for different
+  genes;
+- Test of hypotheses concerning sequence evolution, such as rate
+  constancy and independence among nucleotide or amino acid sites, rate
+  constancy among lineages (the molecular clock), and homogeneity of
+  evolutionary process in multiple genes;
+- Calculation of substitution rates at sites; 
+- Reconstruction of ancestral nucleotide or amino acid sequences;
+- Simulation of nucleotide, codon, and amino acid sequence data sets; 
+- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. 
+
+WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
new file mode 100644
index 00000000000..10c94586d97
--- /dev/null
+++ b/biology/paml/pkg-plist
@@ -0,0 +1,11 @@
+bin/baseml
+bin/basemlg
+bin/chi2 
+bin/codeml
+bin/codemlsites
+bin/evolver
+bin/mcmctree
+bin/pamp
+bin/yn00
+share/doc/paml/pamlDOC.pdf
+@dirrm share/doc/paml