--- a/configure.in
+++ b/configure.in
@@ -649,33 +649,6 @@
 
 
 
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR="7"
-PCRE_MINOR="9"
-PCRE_DATE="11-Apr-2009"
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION="0:1:0"
-PCRE_POSIXLIB_VERSION="0:0:0"
-
-
-
-
 dnl FIXME: This does no longer seem required with Autoconf 2.67?
 dnl Intel MacOSX 10.6 puts X11 in a non-standard place
 dnl AS_IF([test "x${with_x}" != "xno"],
@@ -751,21 +724,6 @@
 
 
 
-dnl "Export" these variables for PCRE
-
-AC_SUBST([HAVE_MEMMOVE])
-AC_SUBST([HAVE_STRERROR])
-AC_SUBST([PCRE_MAJOR])
-AC_SUBST([PCRE_MINOR])
-AC_SUBST([PCRE_DATE])
-AC_SUBST([PCRE_VERSION])
-AC_SUBST([PCRE_LIB_VERSION])
-AC_SUBST([PCRE_POSIXLIB_VERSION])
-AC_SUBST([POSIX_MALLOC_THRESHOLD])
-
-
-
-
 dnl Test if --enable-localforce given
 locallink="no"
 embprefix="/usr/local"
@@ -888,6 +846,13 @@
 AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
 
 
+AS_IF([test "x${enable_systemlibs}" = "xyes"],
+[
+dnl using system libraries
+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
+  )
+])
 
 
 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -10,7 +10,7 @@
 -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leplplot -leexpat \
 -lezlib -lepcre
 else
-CYGWIN_LDVIENNA = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl \
+CYGWIN_LDVIENNA = -lnucleus -lacd -lajaxdb -lensembl \
                 -lajaxg -lajax -leplplot -leexpat -lezlib -lepcre
 endif
 endif
@@ -32,9 +32,7 @@
 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
 	-I../../../ajax/acd -I../../../plplot
 else
-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \
-	$(NLINCLUDES) \
-	-I${embprefix}/include/epcre
+AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
 endif
 
 if ISSHARED
@@ -49,7 +47,7 @@
 -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
  $(NLAIXLIBS) -leplplot
 else
-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
 -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre $(NLAIXLIBS) -leplplot
 endif
 endif
@@ -87,6 +85,7 @@
 endif
 
 liboviennarna_la_LDFLAGS = $(LINKFLAGS)
+liboviennarna_la_LIBADD = -lajax
 
 ovrnaalifold_SOURCES = vrnaalifold.c
 ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
@@ -118,6 +117,6 @@
 	../../../plplot/libeplplot.la \
 	$(XLIB)
 else
-LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
-	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
+LDADD = liboviennarna.la -lnucleus -lacd -lajaxdb \
+	-lensembl -lajaxg -lajax $(NLADD) $(XLIB)
 endif