Initial import of puzzle-4.0.2, a maximum likelihood analysis tool of

molecular sequence data

9 files changed, 112 insertions, 0 deletions

diff --git a/biology/puzzle/Makefile b/biology/puzzle/Makefile
new file mode 100644
index 00000000000..8ca9dd8edc5
--- /dev/null
+++ b/biology/puzzle/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD: Makefile,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+DISTNAME=	puzzle-402
+PKGNAME=	puzzle-4.0.2
+WRKSRC=		${WRKDIR}/${PKGNAME}/src
+CATEGORIES=	biology
+MASTER_SITES=	http://members.tripod.de/korbi/puzzle/ \
+		ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/ \
+		ftp://ftp.pasteur.fr/pub/GenSoft/unix/evolution/Puzzle/ \
+		ftp://iubio.bio.indiana.edu/molbio/evolve/puzzle/ \
+		http://iubio.bio.indiana.edu/soft/molbio/evolve/puzzle/
+
+MAINTAINER=	babafou@babafou.eu.org
+HOMEPAGE=	http://members.tripod.de/korbi/puzzle/
+
+MAKEFILE=	makefile
+ALL_TARGET=	puzzle
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/puzzle ${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/puzzle
+	${INSTALL_DATA} ${WRKDIR}/${PKGNAME}/doc/manual.html ${PREFIX}/share/doc/puzzle
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/puzzle/files/md5 b/biology/puzzle/files/md5
new file mode 100644
index 00000000000..98aa2b37ae1
--- /dev/null
+++ b/biology/puzzle/files/md5
@@ -0,0 +1,3 @@
+$NetBSD: md5,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+MD5 (puzzle-402.tar.gz) = 635ae0594a06a379add882c90d0c616d
diff --git a/biology/puzzle/files/patch-sum b/biology/puzzle/files/patch-sum
new file mode 100644
index 00000000000..6b07c229b89
--- /dev/null
+++ b/biology/puzzle/files/patch-sum
@@ -0,0 +1,5 @@
+$NetBSD: patch-sum,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+MD5 (patch-aa) = 431dbe0506217e4b1772b4e18c839285
+MD5 (patch-ab) = bf25b9a245e28967462928076816d80a
+MD5 (patch-ac) = bff9421d8ba9b763a801b2a8bd888c82
diff --git a/biology/puzzle/patches/patch-aa b/biology/puzzle/patches/patch-aa
new file mode 100644
index 00000000000..921af783c37
--- /dev/null
+++ b/biology/puzzle/patches/patch-aa
@@ -0,0 +1,20 @@
+$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+--- makefile.orig	Sun May 23 15:40:28 1999
++++ makefile	Sun May 23 15:40:42 1999
+@@ -10,11 +10,11 @@
+ 
+ 
+ # ANSI C compiler
+-CC = gcc
+-CFLAGS = -O3 -Wall -pedantic -ansi
++#CC = gcc
++#CFLAGS = -O3 -Wall -pedantic -ansi
+ # Comment out for compiler other than gcc
+-#CC = cc
+-#CFLAGS = -O 
++CC = cc
++CFLAGS = -O 
+ 
+ # ANSI math library
+ LIBFLAGS = -lm
diff --git a/biology/puzzle/patches/patch-ab b/biology/puzzle/patches/patch-ab
new file mode 100644
index 00000000000..343ad02a0e3
--- /dev/null
+++ b/biology/puzzle/patches/patch-ab
@@ -0,0 +1,13 @@
+$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+--- ml.h.orig	Sun May 23 12:08:41 1999
++++ ml.h	Sun May 23 12:08:49 1999
+@@ -165,7 +165,7 @@
+ /* function prototypes of all ml function */
+ 
+ void convfreq(dvector);
+-void radixsort(cmatrix, ivector, int, int, int *);
++void my_radixsort(cmatrix, ivector, int, int, int *);
+ void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int);
+ void countconstantsites(cmatrix, ivector, int, int, int *);
+ void evaluateseqs(void);
diff --git a/biology/puzzle/patches/patch-ac b/biology/puzzle/patches/patch-ac
new file mode 100644
index 00000000000..ff0797222ad
--- /dev/null
+++ b/biology/puzzle/patches/patch-ac
@@ -0,0 +1,22 @@
+$NetBSD: patch-ac,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+
+--- ml1.c.orig	Sun May 23 12:07:15 1999
++++ ml1.c	Sun May 23 12:07:36 1999
+@@ -65,7 +65,7 @@
+ }
+ 
+ /* sort site patters of original input data */
+-void radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
++void my_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
+ 	int *numptrn)
+ {
+ 	int i, j, k, l, n, pass;
+@@ -181,7 +181,7 @@
+ 
+ 	convfreq(Freqtpm); /* make all frequencies slightly different */
+ 	ali = new_ivector(Maxsite);
+-	radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
++	my_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
+ 	Seqpat = new_cmatrix(Maxspc, Numptrn);
+ 	constpat = new_ivector(Numptrn);
+ 	Weight = new_ivector(Numptrn);
diff --git a/biology/puzzle/pkg/COMMENT b/biology/puzzle/pkg/COMMENT
new file mode 100644
index 00000000000..c001d039dde
--- /dev/null
+++ b/biology/puzzle/pkg/COMMENT
@@ -0,0 +1 @@
+Maximum likelihood analysis of molecular sequence data
diff --git a/biology/puzzle/pkg/DESCR b/biology/puzzle/pkg/DESCR
new file mode 100644
index 00000000000..5909faa5f6a
--- /dev/null
+++ b/biology/puzzle/pkg/DESCR
@@ -0,0 +1,20 @@
+PUZZLE is a computer program to reconstruct phylogenetic trees
+from molecular sequence data by maximum likelihood.  It implements
+a fast tree search algorithm, quartet puzzling, that allows
+analysis of large data sets and automatically assigns estimations
+of support to each internal branch.  PUZZLE also computes pairwise
+maximum likelihood distances as well as branch lengths for user
+specified trees.  Branch lengths can also be calculated under the
+clock-assumption.  In addition, PUZZLE offers a novel method,
+likelihood mapping, to investigate the support of a hypothesized
+internal branch without computing an overall tree and to
+visualize the phylogenetic content of a sequence alignment.
+PUZZLE also conducts a number of statistical tests on the data
+set (chi-square test for homogeneity of base composition,
+likelihood ratio to test the clock hypothesis, Kishino-Hasegaw a
+test).  The models of substitution provided by PUZZLE are TN, HKY,
+F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for
+amino acids, and F81 for two-state data.  Rate heterogeneity is
+modelled by a discrete Gamma distribution and by allowing
+invariable sites.  The corresponding parameters can be inferred
+from the data set.
diff --git a/biology/puzzle/pkg/PLIST b/biology/puzzle/pkg/PLIST
new file mode 100644
index 00000000000..3356fd35c39
--- /dev/null
+++ b/biology/puzzle/pkg/PLIST
@@ -0,0 +1,4 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+bin/puzzle
+share/doc/puzzle/manual.html
+@dirrm share/doc/puzzle