- Update to 2.0

PR:		ports/117713
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>

15 files changed, 60 insertions, 406 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index c55a1a33b541..91b64b4ca491 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -6,21 +6,21 @@
 #
 
 PORTNAME=	clustalw
-PORTVERSION=	1.83
+PORTVERSION=	2.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
-DISTNAME=	${PORTNAME}${PORTVERSION}.UNIX
+MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
+DISTNAME=	${PORTNAME}-linux-src-${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	CLUSTAL W Multiple Sequence Alignment Program
 
 WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
 
-MAKEFILE=	makefile
 ALL_TARGET=	# empty
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/clustalw2 ${PREFIX}/bin
+	${LN} -sf clustalw2 ${PREFIX}/bin/clustalw
 	@${MKDIR} ${DATADIR}
 	${INSTALL_DATA} ${WRKSRC}/clustalw_help ${DATADIR}
 
diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo
index 986c13b67e16..01cadf368b09 100644
--- a/biology/clustalw/distinfo
+++ b/biology/clustalw/distinfo
@@ -1,3 +1,3 @@
-MD5 (clustalw1.83.UNIX.tar.gz) = dc240277e5bb14ffc106d4a5fda87752
-SHA256 (clustalw1.83.UNIX.tar.gz) = 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60
-SIZE (clustalw1.83.UNIX.tar.gz) = 166863
+MD5 (clustalw-linux-src-2.0.tar.gz) = 04bb7bad022dad39bafc1db8c6d64446
+SHA256 (clustalw-linux-src-2.0.tar.gz) = e10c456f45f892936903069638271df6fb4bf30a84d0362ce62031f058408ded
+SIZE (clustalw-linux-src-2.0.tar.gz) = 274726
diff --git a/biology/clustalw/files/patch-Makefile b/biology/clustalw/files/patch-Makefile
new file mode 100644
index 000000000000..0c97d76d5b5c
--- /dev/null
+++ b/biology/clustalw/files/patch-Makefile
@@ -0,0 +1,13 @@
+--- Makefile.orig	Wed Aug  8 18:21:23 2007
++++ Makefile	Wed Oct 31 17:35:20 2007
+@@ -51,8 +51,8 @@
+           compiledObjects/RootedClusterTree.o compiledObjects/Iteration.o \
+           compiledObjects/InFileStream.o compiledObjects/ClustalWResources.o
+ 
+-CXX	= g++
+-CXXFLAGS  = -c -O2
++CXX	?= g++
++CXXFLAGS  += -c -DDATADIR=\"${PREFIX}/share/clustalw\"
+ LFLAGS	= -g
+ 
+ clustalw2: $(OBJECTS)
diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa
deleted file mode 100644
index e3f7f4a8a915..000000000000
--- a/biology/clustalw/files/patch-aa
+++ /dev/null
@@ -1,11 +0,0 @@
---- clustalw.c.orig	Thu Feb 13 15:17:15 2003
-+++ clustalw.c	Thu Feb 13 14:50:51 2003
-@@ -34,7 +34,7 @@
- #ifdef MSDOS
-         char *help_file_name = "clustalw.hlp";
- #else
--        char *help_file_name = "clustalw_help";
-+        char *help_file_name = DATADIR "/clustalw_help";
- #endif
- 
- sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/files/patch-ab b/biology/clustalw/files/patch-ab
deleted file mode 100644
index 110e16238cd1..000000000000
--- a/biology/clustalw/files/patch-ab
+++ /dev/null
@@ -1,24 +0,0 @@
---- makefile.orig	Thu Feb 13 15:17:25 2003
-+++ makefile	Thu Feb 13 15:15:48 2003
-@@ -4,15 +4,15 @@
- 	rm *.o
- 
- OBJECTS = interface.o sequence.o showpair.o malign.o \
--  	util.o trees.o gcgcheck.o prfalign.o pairalign.o \
--  	calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
--        readmat.o alnscore.o random.o 
-+	util.o trees.o gcgcheck.o prfalign.o pairalign.o \
-+	calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
-+	readmat.o alnscore.o random.o 
- 
- HEADERS = general.h clustalw.h
- 
--CC	= cc
--CFLAGS  = -c -O
--LFLAGS	= -O -lm 
-+CC	?= cc
-+CFLAGS  += -c -DDATADIR=\"${PREFIX}/share/clustalw\"
-+LFLAGS	= -lm 
- 
- clustalw : $(OBJECTS) amenu.o clustalw.o
- 	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
diff --git a/biology/clustalw/files/patch-ac b/biology/clustalw/files/patch-ac
deleted file mode 100644
index 2cf5496f3631..000000000000
--- a/biology/clustalw/files/patch-ac
+++ /dev/null
@@ -1,137 +0,0 @@
---- interface.c.orig	Thu Feb 13 15:17:33 2003
-+++ interface.c	Thu Feb 13 15:26:28 2003
-@@ -1132,7 +1132,7 @@
- 	/* added for File System Standards  - Francois */
- 	path1=(char *)ckalloc((strlen(path)+64)*sizeof(char));
- 	strcpy(path1,path);
--	strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); 
-+	strcat(path1,DATADIR); 
- 
-         lf=(sint)strlen(fname);
-         deb=path1;
-@@ -1224,7 +1224,7 @@
- 				if(strstr(temp, help_marker)){
- 				  	if(usemenu) {
- 						fprintf(stdout,"\n");
--				    		getstr("Press [RETURN] to continue",lin2);
-+				    		getstr("Press [RETURN] to continue",lin2,MAXLINE);
- 				  	}
- 					fclose(help_file);
- 					return;
-@@ -1236,7 +1236,7 @@
- 			       if(usemenu) {
- 			          if(nlines >= PAGE_LEN) {
- 				     	   fprintf(stdout,"\n");
--			 	  	   getstr("Press [RETURN] to continue or  X  to stop",lin2);
-+			 	  	   getstr("Press [RETURN] to continue or  X  to stop",lin2,MAXLINE);
- 				  	   if(toupper(*lin2) == 'X') {
- 						   fclose(help_file);
- 						   return;
-@@ -1248,7 +1248,7 @@
- 			}
- 			if(usemenu) {
- 				fprintf(stdout,"\n");
--				getstr("Press [RETURN] to continue",lin2);
-+				getstr("Press [RETURN] to continue",lin2,MAXLINE);
- 			}
- 			fclose(help_file);
- 		}
-@@ -1287,7 +1287,7 @@
-                 ++nlines;
-                 if(nlines >= PAGE_LEN) {
-                         fprintf(stdout,"\n");
--                        getstr("Press [RETURN] to continue or  X  to stop",lin2);
-+                        getstr("Press [RETURN] to continue or  X  to stop",lin2,MAXLINE);
-                         if(toupper(*lin2) == 'X') {
-                                 fclose(file);
-                                 return;
-@@ -1298,7 +1298,7 @@
-         }
-         fclose(file);
-         fprintf(stdout,"\n");
--        getstr("Press [RETURN] to continue",lin2);
-+        getstr("Press [RETURN] to continue",lin2,MAXLINE);
- }
- 
- 
-@@ -1747,7 +1747,7 @@
-         FILE *infile;
- 
-         if(usemenu)
--                getstr("Enter name of the matrix file",lin2);
-+                getstr("Enter name of the matrix file",lin2,MAXLINE);
-         else
-                 strcpy(lin2,str);
- 
-@@ -1773,7 +1773,7 @@
-         FILE *infile;
- 
-         if(usemenu)
--                getstr("Enter name of the matrix file",lin2);
-+                getstr("Enter name of the matrix file",lin2,MAXLINE);
-         else
-                 strcpy(lin2,str);
- 
-@@ -2176,7 +2176,7 @@
- 			strcpy(local_prompt,"\n\nEnter new name to avoid overwriting ");
- 			strcat(local_prompt," [%s]: ");          
- 			fprintf(stdout,local_prompt,file_name);
--			gets(temp);
-+			fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
- 			if(*temp != EOS) strcpy(file_name,temp);
- 		}
- 	}
-@@ -2184,7 +2184,7 @@
- 		strcpy(local_prompt,prompt);
- 		strcat(local_prompt," [%s]: ");          
- 		fprintf(stdout,local_prompt,file_name);
--		gets(temp);
-+		fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
- 		if(*temp != EOS) strcpy(file_name,temp);
- 	}
- 
-@@ -2385,7 +2385,7 @@
- 		if (usemenu)
-             	fprintf(stdout,"\nUse the existing GUIDE TREE file,  %s  (y/n) ? [y]: ",
-                                            tree_name);
--                gets(temp);
-+                fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
-                 if(*temp != 'n' && *temp != 'N') {
-                     strcpy(phylip_name,tree_name);
-                     use_tree = TRUE;
-@@ -2617,7 +2617,7 @@
- 
-             fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ",
-                                            phylip_name);
--                	gets(temp);
-+			fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
-                 	if(*temp != EOS)
-                         	strcpy(phylip_name,temp);
-         	}
-@@ -2719,7 +2719,7 @@
- #endif
-             	fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1,  %s  (y/n) ? [y]: ",
-                                            tree_name);
--                gets(temp);
-+                fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
-                 if(*temp != 'n' && *temp != 'N') {
-                     strcpy(p1_tree_name,tree_name);
-                     use_tree1 = TRUE;
-@@ -2745,7 +2745,7 @@
- #endif
-             	fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2,  %s  (y/n) ? [y]: ",
-                                            tree_name);
--                gets(temp);
-+                fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
-                 if(*temp != 'n' && *temp != 'N') {
-                     strcpy(p2_tree_name,tree_name);
-                     use_tree2 = TRUE;
-@@ -4203,7 +4203,7 @@
-   if(usemenu) {
-     fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ",
- 	    parname);
--    gets(temp);
-+    fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS;
-     if(*temp != EOS)
-       strcpy(parname,temp);
-   }
diff --git a/biology/clustalw/files/patch-ae b/biology/clustalw/files/patch-ae
deleted file mode 100644
index c1a976a1eb26..000000000000
--- a/biology/clustalw/files/patch-ae
+++ /dev/null
@@ -1,138 +0,0 @@
---- amenu.c.orig	Thu Feb 13 15:19:00 2003
-+++ amenu.c	Thu Feb 13 15:21:10 2003
-@@ -13,7 +13,8 @@
- static jmp_buf jmpbuf;
- #ifndef VMS
- #ifndef AIX
--#define BADSIG (void (*)())-1
-+/* #define BADSIG (void (*)())-1 */
-+#define BADSIG SIG_ERR
- #endif
- #endif
- 
-@@ -184,7 +185,7 @@
- 		fprintf(stdout,"     H. HELP\n");
- 		fprintf(stdout,"     X. EXIT (leave program)\n\n\n");
- 		
--		getstr("Your choice",lin1);
-+		getstr("Your choice",lin1,MAXLINE);
- 
- 		switch(toupper(*lin1)) {
- 			case '1': seq_input(FALSE);
-@@ -268,7 +269,7 @@
-         fprintf(stdout,"    H.  HELP\n");
-         fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
- 
--        getstr("Your choice",lin1);
-+        getstr("Your choice",lin1,MAXLINE);
-         if(*lin1 == EOS) return;
- 
-         switch(toupper(*lin1))
-@@ -361,7 +362,7 @@
-         fprintf(stdout,"    H.  HELP\n");
-         fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
- 
--        getstr("Your choice",lin1);
-+        getstr("Your choice",lin1,MAXLINE);
-         if(*lin1 == EOS) return;
- 
-         switch(toupper(*lin1))
-@@ -457,7 +458,7 @@
- 		fprintf(stdout,"\n\n");
- 		fprintf(stdout,"     H. HELP\n\n\n");
- 		
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 		if( *lin2 == EOS) { 
- 			return;
- 		}
-@@ -533,7 +534,7 @@
-                 fprintf(stdout,"--\n");
- 
- 
--                getstr("\n\nEnter number (or [RETURN] to exit)",lin2);
-+                getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE);
-                 if(*lin2 == EOS) return(output_struct_penalties);
- 
-         	switch(toupper(*lin2))
-@@ -602,7 +603,7 @@
-         fprintf(stdout,"    H.  HELP\n");
-         fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
- 
--        getstr("Your choice",lin1);
-+        getstr("Your choice",lin1,MAXLINE);
-         if(*lin1 == EOS) return;
- 
-         switch(toupper(*lin1))
-@@ -677,7 +678,7 @@
- 	fprintf(stdout,"\n");
- 	fprintf(stdout,"     H. HELP\n\n\n");	
- 	
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 		if(*lin2 == EOS) return;
- 		
- 		switch(toupper(*lin2)) {
-@@ -766,7 +767,7 @@
- 	fprintf(stdout,"\n");
- 	fprintf(stdout,"     H. HELP\n\n\n");	
- 	
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 		if(*lin2 == EOS) return;
- 		
- 		switch(toupper(*lin2)) {
-@@ -907,7 +908,7 @@
- 
- 		fprintf(stdout,"     H. HELP\n\n\n");
- 		
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 		if( *lin2 == EOS) {
-                         if(dnaflag) {
-                                 dna_pw_go_penalty     = pw_go_penalty;
-@@ -1029,7 +1030,7 @@
-                 fprintf(stdout,"     8. Protein Gap Parameters\n\n");
- 		fprintf(stdout,"     H. HELP\n\n\n");		
- 
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 
- 		if(*lin2 == EOS) {
- 			if(dnaflag) {
-@@ -1122,7 +1123,7 @@
- 		fprintf(stdout,"     5. Toggle End Gap Separation         :%s\n\n",(!use_endgaps) ? "OFF" : "ON");
- 		fprintf(stdout,"     H. HELP\n\n\n");		
- 
--		getstr("Enter number (or [RETURN] to exit)",lin2);
-+		getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE);
- 
- 		if(*lin2 == EOS) return;
- 		
-@@ -1136,7 +1137,7 @@
- 			case '3':
- 				fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues);
- 
--				getstr("Enter residues (or [RETURN] to quit)",lin1);
-+				getstr("Enter residues (or [RETURN] to quit)",lin1,MAXLINE);
-                                 if (*lin1 != EOS) {
-                                         for (i=0;i<strlen(hyd_residues) && i<26;i++) {
-                                         c = lin1[i];
-@@ -1188,7 +1189,7 @@
-                 fprintf(stdout,"--\n");
- 
- 
--                getstr("\n\nEnter number (or [RETURN] to exit)",lin2);
-+                getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE);
-                 if(*lin2 == EOS) return(matn);
- 
-                 i=toupper(*lin2)-'0';
-@@ -1223,7 +1224,7 @@
- 	fprintf(stdout,"\n%s\n",title);
- 	strcpy(line,prompt);
- 	strcat(line, "(y/n) ? [y]");
--	getstr(line,lin2);
-+	getstr(line,lin2,80);
- 	if ((*lin2 != 'n') && (*lin2 != 'N'))
- 		return('y');
- 	else
diff --git a/biology/clustalw/files/patch-af b/biology/clustalw/files/patch-af
deleted file mode 100644
index 50db34932446..000000000000
--- a/biology/clustalw/files/patch-af
+++ /dev/null
@@ -1,11 +0,0 @@
---- clustalw.h.orig	Thu Feb 13 15:21:45 2003
-+++ clustalw.h	Thu Feb 13 15:21:57 2003
-@@ -238,7 +238,7 @@
- char *blank_to_(char *str);
- char *upstr(char *str);
- char *lowstr(char *str);
--void getstr(char *instr, char *outstr);
-+void getstr(char *instr, char *outstr, int len);
- double getreal(char *instr, double minx, double maxx, double def);
- int getint(char *instr, int minx, int maxx, int def);
- void do_system(void);
diff --git a/biology/clustalw/files/patch-ah b/biology/clustalw/files/patch-ah
deleted file mode 100644
index 929da1599634..000000000000
--- a/biology/clustalw/files/patch-ah
+++ /dev/null
@@ -1,11 +0,0 @@
---- sequence.c.orig	Thu Feb 13 15:27:06 2003
-+++ sequence.c	Thu Feb 13 15:27:37 2003
-@@ -924,7 +924,7 @@
- 	static Boolean dnaflag1;
- 	
- 	if(usemenu)
--		getstr("Enter the name of the sequence file",line);
-+		getstr("Enter the name of the sequence file",line,FILENAMELEN+1);
- 	else
- 		strcpy(line,seqname);
- 	if(*line == EOS) return -1;
diff --git a/biology/clustalw/files/patch-ai b/biology/clustalw/files/patch-ai
deleted file mode 100644
index d2f63dc9e0e5..000000000000
--- a/biology/clustalw/files/patch-ai
+++ /dev/null
@@ -1,11 +0,0 @@
---- trees.c.orig	Thu Feb 13 15:52:06 2003
-+++ trees.c	Thu Feb 13 16:19:08 2003
-@@ -1497,7 +1497,7 @@
- 		fprintf(stdout,"\n           or 3) use the PHYLIP package.");
- 		fprintf(stdout,"\n\n");
- 		if (usemenu) 
--			getstr("Press [RETURN] to continue",dummy);
-+			getstr("Press [RETURN] to continue",dummy,10);
- 	}
- 
- 
diff --git a/biology/clustalw/files/patch-aj b/biology/clustalw/files/patch-aj
deleted file mode 100644
index 4e7cb3c21c94..000000000000
--- a/biology/clustalw/files/patch-aj
+++ /dev/null
@@ -1,43 +0,0 @@
---- util.c.orig	Thu Feb 13 16:19:35 2003
-+++ util.c	Thu Feb 13 16:21:40 2003
-@@ -171,10 +171,11 @@
- 	return str;
- }
- 
--void getstr(char *instr,char *outstr)
-+void getstr(char *instr,char *outstr, int len)
- {	
- 	fprintf(stdout,"%s: ",instr);
--	gets(outstr);
-+	fgets(outstr, len, stdin);
-+	outstr[strlen(outstr)-1] = '\0';
- }
- 
- double getreal(char *instr,double minx,double maxx,double def)
-@@ -185,7 +186,7 @@
- 	
- 	while(TRUE) {
- 		fprintf(stdout,"%s (%.1f-%.1f)   [%.1f]: ",instr,minx,maxx,def);
--		gets(line);
-+		fgets(line, MAXLINE, stdin);
- 		status=sscanf(line,"%f",&ret);
- 		if(status == EOF) return def;
- 		if(ret>maxx) {
-@@ -210,7 +211,7 @@
- 	while(TRUE) {
- 		fprintf(stdout,"%s (%d..%d)    [%d]: ",
- 		instr,(pint)minx,(pint)maxx,(pint)def);
--		gets(line);
-+		fgets(line, MAXLINE, stdin);
- 		status=sscanf(line,"%d",&ret);
- 		if(status == EOF) return def;
- 		if(ret>maxx) {
-@@ -230,7 +231,7 @@
- {
- 	char line[MAXLINE];
- 	
--	getstr("\n\nEnter system command",line);
-+	getstr("\n\nEnter system command",line,MAXLINE);
- 	if(*line != EOS)
- 		system(line);
- 	fprintf(stdout,"\n\n");
diff --git a/biology/clustalw/files/patch-general_ClustalWResources.cpp b/biology/clustalw/files/patch-general_ClustalWResources.cpp
new file mode 100644
index 000000000000..998edbc5b93e
--- /dev/null
+++ b/biology/clustalw/files/patch-general_ClustalWResources.cpp
@@ -0,0 +1,11 @@
+--- general/ClustalWResources.cpp.orig	Thu Jul 19 18:44:22 2007
++++ general/ClustalWResources.cpp	Wed Oct 31 17:39:01 2007
+@@ -33,7 +33,7 @@
+     executablePath = ".";
+     
+     //installPath
+-    installPath = ".";
++    installPath = DATADIR;
+     char *env;
+     if ((env = getenv(CLUW_INSTALL_DIR)) != 0) 
+     {
diff --git a/biology/clustalw/files/patch-general_Utility.cpp b/biology/clustalw/files/patch-general_Utility.cpp
new file mode 100644
index 000000000000..1bbb53d99f9a
--- /dev/null
+++ b/biology/clustalw/files/patch-general_Utility.cpp
@@ -0,0 +1,20 @@
+--- general/Utility.cpp.orig	Wed May 23 22:47:41 2007
++++ general/Utility.cpp	Wed Oct 31 17:19:21 2007
+@@ -144,7 +144,7 @@
+     while (true)
+     {
+         fprintf(stdout, "%s (%.1f-%.1f)   [%.1f]: ", instr, minx, maxx, def);
+-        gets(line);
++        fgets(line, 1024, stdin);
+         status = sscanf(line, "%f", &ret);
+         if (status == EOF)
+         {
+@@ -181,7 +181,7 @@
+     while (true)
+     {
+         fprintf(stdout, "%s (%d..%d)    [%d]: ", instr, minx, maxx, def);
+-        gets(line);
++        fgets(line, 1024, stdin);
+         status = sscanf(line, "%d", &ret);
+         if (status == EOF)
+         {
diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr
index f63c0c96b776..82a997b506ef 100644
--- a/biology/clustalw/pkg-descr
+++ b/biology/clustalw/pkg-descr
@@ -1,24 +1,19 @@
                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:
+Clustal W is a multiple alignment program for DNA or proteins.
+Clustal W was written by Des Higgins (des@chah.ucc.ie), Julie Thompson
+(julie@IGBMC.u-strasbg.fr), and Toby Gibson (Gibson@EMBL-Heidelberg.DE).
+Version 2.0 has been completely rewritten in C++.
 
+Original Paper:
     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.
     
+Tips:
     Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using
 CLUSTAL for multiple sequence alignments. Methods in Enzymology 266:
 383-402.
 
-WWW: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
+WWW: http://bips.u-strasbg.fr/fr/Documentation/ClustalX/
diff --git a/biology/clustalw/pkg-plist b/biology/clustalw/pkg-plist
index 32ff2fc3ac77..8d07bcec1a07 100644
--- a/biology/clustalw/pkg-plist
+++ b/biology/clustalw/pkg-plist
@@ -1,3 +1,4 @@
 bin/clustalw
+bin/clustalw2
 share/clustalw/clustalw_help
 @dirrm share/clustalw