--- Makefile.in.orig	2009-07-07 14:58:30.000000000 -0500
+++ Makefile.in	2012-12-02 03:37:37.000000000 -0600
@@ -6,7 +6,7 @@
           -DPROF_HMM_TRANS=PLAN9      \
           -DPAIR_HMM_STATES=SPACE5    \
           -DPAIR_HMM_TRANS=ALL_TRANS
-LIBS    = @LIBS@
+LIBS    = @LIBS@ @LDFLAGS@
 
 
 # assorted variables