Adding clustalw version 1.81.

A CLUSTAL W Multiple Sequence Alignment Program.

PR:		19746
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>

6 files changed, 66 insertions, 0 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
new file mode 100644
index 0000000..5cedd67
--- /dev/null
+++ b/biology/clustalw/Makefile
@@ -0,0 +1,26 @@
+# New ports collection makefile for:	clustalw
+# Date created:				6 July 2000
+# Whom:					dbader@eece.unm.edu
+#
+# $FreeBSD$
+#
+
+PORTNAME=	clustalw
+PORTVERSION=	1.81
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
+DISTNAME=	clustalw1.81.UNIX
+
+MAINTAINER=	dbader@eece.unm.edu
+
+WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
+
+do-build:
+		cd ${WRKSRC} ; ${MAKE} -f makefile
+
+do-install:
+		${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
+		${MKDIR} ${PREFIX}/share/${PORTNAME}
+		${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME}
+
+.include <bsd.port.mk>
diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo
new file mode 100644
index 0000000..030d310
--- /dev/null
+++ b/biology/clustalw/distinfo
@@ -0,0 +1 @@
+MD5 (clustalw1.81.UNIX.tar.gz) = f239ed842186606ef62529720655ab99
diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa
new file mode 100644
index 0000000..d404277
--- /dev/null
+++ b/biology/clustalw/files/patch-aa
@@ -0,0 +1,11 @@
+--- clustalw.c-orig	Wed Jun  7 01:50:05 2000
++++ clustalw.c	Thu Jul  6 20:19:31 2000
+@@ -33,7 +33,7 @@
+ #ifdef MSDOS
+         char *help_file_name = "clustalw.hlp";
+ #else
+-        char *help_file_name = "clustalw_help";
++        char *help_file_name = "/usr/local/share/clustalw/clustalw_help";
+ #endif
+ 
+ sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/pkg-comment b/biology/clustalw/pkg-comment
new file mode 100644
index 0000000..96dce0a
--- /dev/null
+++ b/biology/clustalw/pkg-comment
@@ -0,0 +1 @@
+CLUSTAL W Multiple Sequence Alignment Program
diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr
new file mode 100644
index 0000000..fcb3931
--- /dev/null
+++ b/biology/clustalw/pkg-descr
@@ -0,0 +1,24 @@
+               CLUSTAL W Multiple Sequence Alignment Program
+
+ClustalW was written by Des Higgins (now at University College, Cork,
+Ireland) (des@chah.ucc.ie), Julie Thompson (julie@IGBMC.u-strasbg.fr),
+Toby Gibson, (Gibson@EMBL-Heidelberg.DE), and Franc'ois Jeanmougin
+(pingouin@igbmc.u-strasbg.fr). It is a complete rewrite and upgrade of
+the Clustal and ClustalV packages. which were developed by Des
+Higgins. New features include the ability to detect read different
+input formats (NBRF/PIR, Fasta, EMBL/Swissprot); align old alignments;
+produce phylogenetic trees after alignment (Neighbor Joining trees
+with a bootstrap option); write different alignment formats (Clustal,
+NBRF/PIR, GCG, PHYLIP); full command line interface. It is described
+in the following papers:
+
+    Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W:
+improving the sensitivity of progressive multiple sequence alignment
+through sequence weighting, positions-specific gap penalties and
+weight matrix choice. Nucleic Acids Research 22: 4673-4680.
+    
+    Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using
+CLUSTAL for multiple sequence alignments. Methods in Enzymology 266:
+383-402.
+
+  See URL: www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
diff --git a/biology/clustalw/pkg-plist b/biology/clustalw/pkg-plist
new file mode 100644
index 0000000..32ff2fc
--- /dev/null
+++ b/biology/clustalw/pkg-plist
@@ -0,0 +1,3 @@
+bin/clustalw
+share/clustalw/clustalw_help
+@dirrm share/clustalw