Update to 1.83.

PR:		48264
Submitted by:	David A. Bader <dbader@eece.unm.edu>

13 files changed, 179 insertions, 182 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index ffd6ce7e1be4..920c77e970b8 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -6,13 +6,13 @@
 #
 
 PORTNAME=	clustalw
-PORTVERSION=	1.82
-PORTREVISION=	2
+PORTVERSION=	1.83
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
 DISTNAME=	${PORTNAME}${PORTVERSION}.UNIX
 
 MAINTAINER=	dbader@eece.unm.edu
+COMMENT=	CLUSTAL W Multiple Sequence Alignment Program
 
 WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
 
diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo
index 4a5de2b1cc1a..a67b9478f845 100644
--- a/biology/clustalw/distinfo
+++ b/biology/clustalw/distinfo
@@ -1 +1 @@
-MD5 (clustalw1.82.UNIX.tar.gz) = 8171ec890182383000bdb83de3022ca2
+MD5 (clustalw1.83.UNIX.tar.gz) = dc240277e5bb14ffc106d4a5fda87752
diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa
index 56e36ffce6ba..e3f7f4a8a915 100644
--- a/biology/clustalw/files/patch-aa
+++ b/biology/clustalw/files/patch-aa
@@ -1,6 +1,6 @@
---- clustalw.c-orig	Wed Jun  7 01:50:05 2000
-+++ clustalw.c	Thu Jul  6 20:19:31 2000
-@@ -33,7 +33,7 @@
+--- 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
diff --git a/biology/clustalw/files/patch-ab b/biology/clustalw/files/patch-ab
index 03e9eccaae85..110e16238cd1 100644
--- a/biology/clustalw/files/patch-ab
+++ b/biology/clustalw/files/patch-ab
@@ -1,6 +1,15 @@
---- makefile.orig	Wed Jun  7 16:55:06 2000
-+++ makefile	Tue Aug  8 02:30:53 2000
-@@ -10,9 +10,9 @@
+--- 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
  
diff --git a/biology/clustalw/files/patch-ac b/biology/clustalw/files/patch-ac
index fc4431f3b68f..57656a482e8b 100644
--- a/biology/clustalw/files/patch-ac
+++ b/biology/clustalw/files/patch-ac
@@ -1,6 +1,6 @@
---- interface.c.orig	Wed Jun  7 16:50:07 2000
-+++ interface.c	Tue Aug  8 03:11:33 2000
-@@ -1078,7 +1078,7 @@
+--- 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);
@@ -9,3 +9,129 @@
  
          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) 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) 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 != '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)
+                         	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 != '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 != '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)
+       strcpy(parname,temp);
+   }
diff --git a/biology/clustalw/files/patch-ae b/biology/clustalw/files/patch-ae
index b9e3678ea31b..c1a976a1eb26 100644
--- a/biology/clustalw/files/patch-ae
+++ b/biology/clustalw/files/patch-ae
@@ -1,5 +1,5 @@
---- amenu.c-orig	Tue Feb  6 03:15:01 2001
-+++ amenu.c	Thu Mar 21 10:19:02 2002
+--- 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
@@ -10,7 +10,7 @@
  #endif
  #endif
  
-@@ -176,7 +177,7 @@
+@@ -184,7 +185,7 @@
  		fprintf(stdout,"     H. HELP\n");
  		fprintf(stdout,"     X. EXIT (leave program)\n\n\n");
  		
@@ -19,7 +19,7 @@
  
  		switch(toupper(*lin1)) {
  			case '1': seq_input(FALSE);
-@@ -260,7 +261,7 @@
+@@ -268,7 +269,7 @@
          fprintf(stdout,"    H.  HELP\n");
          fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
  
@@ -28,7 +28,7 @@
          if(*lin1 == EOS) return;
  
          switch(toupper(*lin1))
-@@ -353,7 +354,7 @@
+@@ -361,7 +362,7 @@
          fprintf(stdout,"    H.  HELP\n");
          fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
  
@@ -37,7 +37,7 @@
          if(*lin1 == EOS) return;
  
          switch(toupper(*lin1))
-@@ -449,7 +450,7 @@
+@@ -457,7 +458,7 @@
  		fprintf(stdout,"\n\n");
  		fprintf(stdout,"     H. HELP\n\n\n");
  		
@@ -46,7 +46,7 @@
  		if( *lin2 == EOS) { 
  			return;
  		}
-@@ -525,7 +526,7 @@
+@@ -533,7 +534,7 @@
                  fprintf(stdout,"--\n");
  
  
@@ -55,7 +55,7 @@
                  if(*lin2 == EOS) return(output_struct_penalties);
  
          	switch(toupper(*lin2))
-@@ -594,7 +595,7 @@
+@@ -602,7 +603,7 @@
          fprintf(stdout,"    H.  HELP\n");
          fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");
  
@@ -64,7 +64,7 @@
          if(*lin1 == EOS) return;
  
          switch(toupper(*lin1))
-@@ -669,7 +670,7 @@
+@@ -677,7 +678,7 @@
  	fprintf(stdout,"\n");
  	fprintf(stdout,"     H. HELP\n\n\n");	
  	
@@ -73,7 +73,7 @@
  		if(*lin2 == EOS) return;
  		
  		switch(toupper(*lin2)) {
-@@ -752,7 +753,7 @@
+@@ -766,7 +767,7 @@
  	fprintf(stdout,"\n");
  	fprintf(stdout,"     H. HELP\n\n\n");	
  	
@@ -82,7 +82,7 @@
  		if(*lin2 == EOS) return;
  		
  		switch(toupper(*lin2)) {
-@@ -886,7 +887,7 @@
+@@ -907,7 +908,7 @@
  
  		fprintf(stdout,"     H. HELP\n\n\n");
  		
@@ -91,7 +91,7 @@
  		if( *lin2 == EOS) {
                          if(dnaflag) {
                                  dna_pw_go_penalty     = pw_go_penalty;
-@@ -1008,7 +1009,7 @@
+@@ -1029,7 +1030,7 @@
                  fprintf(stdout,"     8. Protein Gap Parameters\n\n");
  		fprintf(stdout,"     H. HELP\n\n\n");		
  
@@ -100,7 +100,7 @@
  
  		if(*lin2 == EOS) {
  			if(dnaflag) {
-@@ -1101,7 +1102,7 @@
+@@ -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");		
  
@@ -109,7 +109,7 @@
  
  		if(*lin2 == EOS) return;
  		
-@@ -1115,7 +1116,7 @@
+@@ -1136,7 +1137,7 @@
  			case '3':
  				fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues);
  
@@ -118,7 +118,7 @@
                                  if (*lin1 != EOS) {
                                          for (i=0;i<strlen(hyd_residues) && i<26;i++) {
                                          c = lin1[i];
-@@ -1167,7 +1168,7 @@
+@@ -1188,7 +1189,7 @@
                  fprintf(stdout,"--\n");
  
  
@@ -127,7 +127,7 @@
                  if(*lin2 == EOS) return(matn);
  
                  i=toupper(*lin2)-'0';
-@@ -1202,7 +1203,7 @@
+@@ -1223,7 +1224,7 @@
  	fprintf(stdout,"\n%s\n",title);
  	strcpy(line,prompt);
  	strcat(line, "(y/n) ? [y]");
diff --git a/biology/clustalw/files/patch-af b/biology/clustalw/files/patch-af
index 102413fb84c6..50db34932446 100644
--- a/biology/clustalw/files/patch-af
+++ b/biology/clustalw/files/patch-af
@@ -1,6 +1,6 @@
---- clustalw.h-orig	Thu Mar 21 10:15:28 2002
-+++ clustalw.h	Thu Mar 21 10:15:43 2002
-@@ -234,7 +234,7 @@
+--- 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);
diff --git a/biology/clustalw/files/patch-ag b/biology/clustalw/files/patch-ag
deleted file mode 100644
index 9cde8d9d019d..000000000000
--- a/biology/clustalw/files/patch-ag
+++ /dev/null
@@ -1,128 +0,0 @@
---- interface.c-orig	Thu Mar 21 10:19:26 2002
-+++ interface.c	Thu Mar 21 10:22:18 2002
-@@ -1170,7 +1170,7 @@
- 				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;
-@@ -1182,7 +1182,7 @@
- 			       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;
-@@ -1194,7 +1194,7 @@
- 			}
- 			if(usemenu) {
- 				fprintf(stdout,"\n");
--				getstr("Press [RETURN] to continue",lin2);
-+				getstr("Press [RETURN] to continue",lin2,MAXLINE);
- 			}
- 			fclose(help_file);
- 		}
-@@ -1232,7 +1232,7 @@
-                 ++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;
-@@ -1243,7 +1243,7 @@
-         }
-         fclose(file);
-         fprintf(stdout,"\n");
--        getstr("Press [RETURN] to continue",lin2);
-+        getstr("Press [RETURN] to continue",lin2,MAXLINE);
- }
- 
- 
-@@ -1692,7 +1692,7 @@
-         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);
- 
-@@ -1718,7 +1718,7 @@
-         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);
- 
-@@ -2121,7 +2121,7 @@
- 			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) strcpy(file_name,temp);
- 		}
- 	}
-@@ -2129,7 +2129,7 @@
- 		strcpy(local_prompt,prompt);
- 		strcat(local_prompt," [%s]: ");          
- 		fprintf(stdout,local_prompt,file_name);
--		gets(temp);
-+		fgets(temp,FILENAMELEN+1,stdin);
- 		if(*temp != EOS) strcpy(file_name,temp);
- 	}
- 
-@@ -2335,7 +2335,7 @@
- 		if (usemenu)
-             	fprintf(stdout,"\nUse the existing GUIDE TREE file,  %s  (y/n) ? [y]: ",
-                                            tree_name);
--                gets(temp);
-+                fgets(temp,MAXLINE,stdin);
-                 if(*temp != 'n' && *temp != 'N') {
-                     strcpy(phylip_name,tree_name);
-                     use_tree = TRUE;
-@@ -2567,7 +2567,7 @@
- 
-             fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ",
-                                            phylip_name);
--                	gets(temp);
-+                	fgets(temp,MAXLINE,stdin);
-                 	if(*temp != EOS)
-                         	strcpy(phylip_name,temp);
-         	}
-@@ -2676,7 +2676,7 @@
- #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 != 'n' && *temp != 'N') {
-                     strcpy(p1_tree_name,tree_name);
-                     use_tree1 = TRUE;
-@@ -2702,7 +2702,7 @@
- #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 != 'n' && *temp != 'N') {
-                     strcpy(p2_tree_name,tree_name);
-                     use_tree2 = TRUE;
-@@ -3730,7 +3730,7 @@
- 	if(usemenu) {
-         	fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ",
-                                            parname);
--               	gets(temp);
-+               	fgets(temp,FILENAMELEN+1,stdin);
-                	if(*temp != EOS)
-                        	strcpy(parname,temp);
-        	}
diff --git a/biology/clustalw/files/patch-ah b/biology/clustalw/files/patch-ah
index e16d4f3b28d9..929da1599634 100644
--- a/biology/clustalw/files/patch-ah
+++ b/biology/clustalw/files/patch-ah
@@ -1,6 +1,6 @@
---- sequence.c-orig	Thu Mar 21 10:22:35 2002
-+++ sequence.c	Thu Mar 21 10:22:53 2002
-@@ -922,7 +922,7 @@
+--- 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)
diff --git a/biology/clustalw/files/patch-ai b/biology/clustalw/files/patch-ai
index a228ed5b1eb4..d2f63dc9e0e5 100644
--- a/biology/clustalw/files/patch-ai
+++ b/biology/clustalw/files/patch-ai
@@ -1,6 +1,6 @@
---- trees.c-orig	Thu Mar 21 10:23:04 2002
-+++ trees.c	Thu Mar 21 10:23:20 2002
-@@ -845,7 +845,7 @@
+--- 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) 
diff --git a/biology/clustalw/files/patch-aj b/biology/clustalw/files/patch-aj
index d5881bdb2c03..4e7cb3c21c94 100644
--- a/biology/clustalw/files/patch-aj
+++ b/biology/clustalw/files/patch-aj
@@ -1,6 +1,6 @@
---- util.c-orig	Thu Mar 21 10:15:59 2002
-+++ util.c	Thu Mar 21 10:17:11 2002
-@@ -171,10 +171,10 @@
+--- 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;
  }
  
@@ -10,10 +10,11 @@
  	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 +185,7 @@
+@@ -185,7 +186,7 @@
  	
  	while(TRUE) {
  		fprintf(stdout,"%s (%.1f-%.1f)   [%.1f]: ",instr,minx,maxx,def);
@@ -22,7 +23,7 @@
  		status=sscanf(line,"%f",&ret);
  		if(status == EOF) return def;
  		if(ret>maxx) {
-@@ -210,7 +210,7 @@
+@@ -210,7 +211,7 @@
  	while(TRUE) {
  		fprintf(stdout,"%s (%d..%d)    [%d]: ",
  		instr,(pint)minx,(pint)maxx,(pint)def);
@@ -31,7 +32,7 @@
  		status=sscanf(line,"%d",&ret);
  		if(status == EOF) return def;
  		if(ret>maxx) {
-@@ -230,7 +230,7 @@
+@@ -230,7 +231,7 @@
  {
  	char line[MAXLINE];
  	
diff --git a/biology/clustalw/files/patch-ak b/biology/clustalw/files/patch-ak
deleted file mode 100644
index 8bad3e0dfbbb..000000000000
--- a/biology/clustalw/files/patch-ak
+++ /dev/null
@@ -1,10 +0,0 @@
---- util.c-orig	Fri Mar 22 09:30:46 2002
-+++ util.c	Fri Mar 22 09:31:33 2002
-@@ -175,6 +175,7 @@
- {	
- 	fprintf(stdout,"%s: ",instr);
- 	fgets(outstr, len, stdin);
-+	outstr[strlen(outstr)-1] = '\0';
- }
- 
- double getreal(char *instr,double minx,double maxx,double def)
diff --git a/biology/clustalw/pkg-comment b/biology/clustalw/pkg-comment
deleted file mode 100644
index 96dce0a32542..000000000000
--- a/biology/clustalw/pkg-comment
+++ /dev/null
@@ -1 +0,0 @@
-CLUSTAL W Multiple Sequence Alignment Program