--- /dev/null
+
+CXXOBJS = MSA.o MSAGuideTree.o MSAClusterTree.o MSAPartProbs.o MSAReadMatrix.o main.o
+
+OPENMP = -fopenmp
+CXX = g++
+COMMON_FLAGS = -O3 $(OPENMP) -Wall -funroll-loops -I . -I /usr/include
+CXXFLAGS = $(COMMON_FLAGS)
+
+EXEC = msaprobs
+
+all: $(CXXOBJS)
+ $(CXX) $(CXXFLAGS) -o $(EXEC) $(CXXOBJS) $(NVCCOBJS) $(NVCCLIBS)
+ strip $(EXEC)
+clean:
+ rm -rf *.o $(EXEC)
+