diff -ur mmseq_0.9.9/Makefile mmseq_0.9.9.new/Makefile
--- mmseq_0.9.9/Makefile	2011-03-18 00:25:53.000000000 +0000
+++ mmseq_0.9.9.new/Makefile	2011-04-09 16:46:16.445406767 +0100
@@ -26,19 +26,19 @@
 .PHONY : all
 
 mmseq : sokal.o mmseq.cpp
-	$(CXX) ${MACROS} -fopenmp -O3 sokal.o mmseq.cpp -o mmseq ${LIBS}
+	$(CXX) ${MACROS} $(CXXFLAGS) -fopenmp sokal.o mmseq.cpp -o mmseq ${LIBS}
 
 static: sokal.o mmseq.cpp
 	$(CXX) ${MACROS} ${STATICFLAG} -fopenmp -O3 sokal.o mmseq.cpp -o ${STATICBIN} ${STATICLIBS}
 
 sokal.o : sokal.cc sokal.hh
-	$(CXX) -c sokal.cc
+	$(CXX) $(CXXFLAGS) -c sokal.cc
 
 fasta.o : fasta.c fasta.h
-	$(CC) -c fasta.c
+	$(CC) $(CXXFLAGS) -c fasta.c
 
 bam2hits : fasta.o bam2hits.cpp
-	${CXX} ${MACROS} -fopenmp -O3 fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H}
+	${CXX} ${MACROS} $(CXXFLAGS) -fopenmp fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H}
 
 hpc : mmseq_hpc bam2hits_hpc
 .PHONY : all