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  nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o \
  outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o \
  phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o \
  profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o \
  realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o \
  refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o \
  scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o \
  setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o \
  subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o \
  tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o \
  validateids.o vtml2.o writescorefile.o

.SUFFIXES: .cpp .o

.cpp.o:
	@echo Compiling $<
	@$(CXX) $(CXXFLAGS) -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -o $@ $<

muscle: $(objects)
	@echo Linking $@
	@$(CXX) $(LDFLAGS) -g -o $@ $(objects)