--- exonerate-2.2.0.orig/configure.in	2008-10-17 12:04:33.000000000 +0200
+++ exonerate-2.2.0/configure.in	2009-10-10 16:42:40.843909374 +0200
@@ -289,7 +289,7 @@
 if test "$enable_pthreads" = yes; then
     echo "Using PTHREADS"
     CFLAGS="$CFLAGS -DUSE_PTHREADS"
-    LDFLAGS="$LDFLAGS -lpthread"
+    LIBS="$LIBS -lpthread"
 elif test "$enable_pthreads" = no; then
     echo "Not using pthreads"
 else
--- exonerate-2.2.0.orig/configure	2008-10-17 12:04:52.000000000 +0200
+++ exonerate-2.2.0/configure	2009-10-10 16:52:04.159444837 +0200
@@ -4569,7 +4569,7 @@
 if test "$enable_pthreads" = yes; then
     echo "Using PTHREADS"
     CFLAGS="$CFLAGS -DUSE_PTHREADS"
-    LDFLAGS="$LDFLAGS -lpthread"
+    LIBS="$LIBS -lpthread"
 elif test "$enable_pthreads" = no; then
     echo "Not using pthreads"
 else