diff --git a/biology/babel/Makefile b/biology/babel/Makefile
index e4bca3550e74..48304650b902 100644
--- a/biology/babel/Makefile
+++ b/biology/babel/Makefile
@@ -7,13 +7,13 @@ PORTREVISION=	4
 CATEGORIES=	biology converters
 MASTER_SITES=	http://smog.com/chem/babel/files/ \
 		http://www.ccl.net/cca/software/UNIX/babel/
-EXTRACT_SUFX=	.tar.Z
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Converts among various molecular file formats
 
 CONFLICTS_INSTALL=	openbabel-*
 
+USES=		tar:Z
 MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
 
 PLIST_FILES+=	bin/babel libexec/babel
diff --git a/biology/babel/files/patch-ab b/biology/babel/files/patch-menus.c
similarity index 100%
rename from biology/babel/files/patch-ab
rename to biology/babel/files/patch-menus.c
diff --git a/biology/p5-AcePerl/files/patch-ac b/biology/p5-AcePerl/files/patch-Makefile.PL
similarity index 100%
rename from biology/p5-AcePerl/files/patch-ac
rename to biology/p5-AcePerl/files/patch-Makefile.PL
diff --git a/biology/p5-AcePerl/files/patch-ab b/biology/p5-AcePerl/files/patch-acelib_memsubs.c
similarity index 100%
rename from biology/p5-AcePerl/files/patch-ab
rename to biology/p5-AcePerl/files/patch-acelib_memsubs.c
diff --git a/biology/p5-AcePerl/files/patch-aa b/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
similarity index 62%
rename from biology/p5-AcePerl/files/patch-aa
rename to biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
index 1bcb9d110568..376d287b34d2 100644
--- a/biology/p5-AcePerl/files/patch-aa
+++ b/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
@@ -1,15 +1,3 @@
---- acelib/wh/mystdlib.h.orig	Mon Jul 16 23:04:45 2001
-+++ acelib/wh/mystdlib.h	Mon Aug 13 12:42:25 2001
-@@ -161,7 +161,8 @@
- #endif
- 
- #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
--	defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS)
-+	defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) || \
-+	defined(FREEBSD)
- 
- #ifdef WIN32
- #include <mbctype.h>
 --- acelib/wh/mydirent.h.orig	Mon Jul 16 23:04:45 2001
 +++ acelib/wh/mydirent.h	Mon Aug 13 12:41:59 2001
 @@ -55,7 +55,7 @@
diff --git a/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h b/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
new file mode 100644
index 000000000000..09c42b7c0fee
--- /dev/null
+++ b/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
@@ -0,0 +1,12 @@
+--- acelib/wh/mystdlib.h.orig	Mon Jul 16 23:04:45 2001
++++ acelib/wh/mystdlib.h	Mon Aug 13 12:42:25 2001
+@@ -161,7 +161,8 @@
+ #endif
+ 
+ #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
+-	defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS)
++	defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) || \
++	defined(FREEBSD)
+ 
+ #ifdef WIN32
+ #include <mbctype.h>
diff --git a/biology/povchem/files/patch-ab b/biology/povchem/files/patch-povchem.c
similarity index 100%
rename from biology/povchem/files/patch-ab
rename to biology/povchem/files/patch-povchem.c
diff --git a/biology/povchem/files/patch-ac b/biology/povchem/files/patch-povchem.cfg
similarity index 100%
rename from biology/povchem/files/patch-ac
rename to biology/povchem/files/patch-povchem.cfg
diff --git a/biology/psi88/files/patch-aa b/biology/psi88/files/patch-src_makefile
similarity index 100%
rename from biology/psi88/files/patch-aa
rename to biology/psi88/files/patch-src_makefile
diff --git a/biology/psi88/files/patch-ba b/biology/psi88/files/patch-unix_rpsi1
similarity index 100%
rename from biology/psi88/files/patch-ba
rename to biology/psi88/files/patch-unix_rpsi1
diff --git a/biology/psi88/files/patch-bb b/biology/psi88/files/patch-unix_rpsi2
similarity index 100%
rename from biology/psi88/files/patch-bb
rename to biology/psi88/files/patch-unix_rpsi2