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#Makefile modified for use in ARB by Arne Boeckmann (aboeckma@mpi-bremen.de)
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LIBDIR = $(ARBHOME)/lib/mafft
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BINDIR = $(ARBHOME)/bin
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#MNO_CYGWIN = -mno-cygwin
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#ENABLE_MULTITHREAD = -Denablemultithread
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# Comment out the above line if your compiler
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# does not support TLS (thread-local strage).
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# if you have icc, use this.
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#CFLAGS = -O0 -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
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#CFLAGS = -O0 -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark
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MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
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ifdef ENABLE_MULTITHREAD
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PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
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pair2hat3s multi2hat3s rnatest pairash addsingle \
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splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
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seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu setdirection makedirectionlist version
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SCRIPTS = mafft mafft-homologs.rb
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OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o
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OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o
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OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o
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OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o
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OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o
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OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o
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OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o
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OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
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OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
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OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
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multi2hat3s.o defs.o fft.o fftFunctions.o
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OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
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pair2hat3s.o defs.o fft.o fftFunctions.o
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OBJRNATEST = mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o \
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rna.o rnatest.o defs.o fft.o fftFunctions.o
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OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
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pairash.o defs.o fft.o fftFunctions.o
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OBJPAIRLOCALALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
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pairlocalalign.o defs.o fft.o fftFunctions.o
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OBJDUMMY = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o
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OBJSPLITFROMALN = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
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OBJSPLITTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o
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OBJSPLITTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
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OBJSPLITTBFASTP = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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Lalign11.o defs.o fft.o fftFunctions.o
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OBJDISTTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o
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OBJMAKEDIRECTIONLIST = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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Lalign11.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o
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OBJTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
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tbfast.o defs.o fft.o fftFunctions.o addfunctions.o
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OBJADDSINGLE = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
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addsingle.o defs.o fft.o fftFunctions.o addfunctions.o
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OBJTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o MSalignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
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tbfast2.o defs.o fft.o fftFunctions.o
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OBJSETCORE = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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setcore.o defs.o fft.o fftFunctions.o
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OBJTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o \
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tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o
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OBJDVTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \
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tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o
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OBJGETLAG = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
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getlag.o defs.o fft.o fftFunctions.o
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OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o
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OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
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OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
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OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o
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OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o
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OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o
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OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o
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OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o
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OBJDNDPRESCORE = dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o
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OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
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SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
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OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o
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HEADER = mltaln.h mtxutl.h
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MANPAGES = mafft.1 mafft-homologs.1
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all : $(PROGS) $(SCRIPTS)
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cp $(SCRIPTS) ../scripts
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chmod 755 ../scripts/*
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cp $(PROGS) ../binaries
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chmod 755 ../binaries/*
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cp $(MANPAGES) ../binaries
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univscript: univscript.tmpl Makefile
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sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
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mafft: mafft.tmpl mltaln.h
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sed 's:_LIBDIR:$$ARBHOME/lib/mafft:' mafft.tmpl > mafft
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mafft-homologs.rb: mafft-homologs.tmpl
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# cp mafft-homologs.tmpl mafft-homologs.rb
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sed 's:_BINDIR:\$$ARBHOME/bin:' mafft-homologs.tmpl > mafft-homologs.rb
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mltaln.h : functions.h
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version : version.c mltaln.h
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$(CC) -o $@ version.c $(MYCFLAGS)
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tbfast : $(OBJTBFAST)
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$(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
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addsingle : $(OBJADDSINGLE)
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$(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS)
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tbfast2 : $(OBJTBFAST2)
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$(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
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disttbfast : $(OBJDISTTBFAST)
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$(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
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makedirectionlist : $(OBJMAKEDIRECTIONLIST)
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$(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS)
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splittbfast : $(OBJSPLITTBFAST)
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$(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
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splitfromaln : $(OBJSPLITFROMALN)
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$(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
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splittbfast2 : $(OBJSPLITTBFAST2)
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$(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
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$(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
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setcore : $(OBJSETCORE)
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$(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
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countlen : $(OBJCOUNTLEN)
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$(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
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seq2regtable : $(OBJSEQ2REGTABLE)
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$(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
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regtable2seq : $(OBJREGTABLE2SEQ)
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$(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
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setdirection : $(OBJSETDIRECTION)
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$(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS)
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replaceu : $(OBJREPLACEU)
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$(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
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restoreu : $(OBJRESTOREU)
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$(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
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$(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
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mccaskillwrap : $(OBJMCCASKILLWRAP)
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$(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
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contrafoldwrap : $(OBJCONTRAFOLDWRAP)
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$(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
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pairlocalalign : $(OBJPAIRLOCALALIGN)
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$(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
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pairash : $(OBJPAIRASH)
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$(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
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rnatest : $(OBJRNATEST)
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$(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
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pair2hat3s : $(OBJPAIR2HAT3S)
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$(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
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multi2hat3s : $(OBJMULTI2HAT3S)
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$(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
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getlag : $(OBJGETLAG)
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$(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
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$(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
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dvtditr : $(OBJDVTDITR)
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$(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
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mafft-profile : $(OBJGALN)
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$(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
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gapfill : $(OBJGAPFILL)
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$(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
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dndfast4 : $(OBJDNDFAST4)
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$(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
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dndfast5 : $(OBJDNDFAST5)
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$(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
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dndfast6 : $(OBJDNDFAST6)
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$(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
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dndfast7 : $(OBJDNDFAST7)
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$(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
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dndblast : $(OBJDNDBLAST)
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$(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
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dndfast3 : $(OBJDNDFAST3)
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$(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
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triplet : $(OBJTRIPLET)
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$(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
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triplet3 : $(OBJTRIPLET3)
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$(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
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sextet3 : $(OBJSEXTET3)
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$(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
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sextet4 : $(OBJSEXTET4)
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$(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
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sextet5 : $(OBJSEXTET5)
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$(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
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mafft-distance : $(OBJDISTANCE)
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$(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
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triplet5 : $(OBJTRIPLET5)
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$(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
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triplet6 : $(OBJTRIPLET6)
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$(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
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octet4 : $(OBJOCTET4)
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$(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
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dndpre : $(OBJDNDPRE)
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$(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
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dndpre2 : $(OBJDNDPRESCORE)
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$(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
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$(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
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genMtx : $(OBJGENMTX)
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$(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
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gapfill.o : gapfill.c $(HEADER)
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$(CC) $(MYCFLAGS) -c gapfill.c
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mltaln9.o : mltaln9.c $(HEADER)
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$(CC) $(MYCFLAGS) -c mltaln9.c
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tddis.o : tddis.c $(HEADER)
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$(CC) $(MYCFLAGS) -c tddis.c
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constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER)
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$(CC) $(MYCFLAGS) -c constants.c
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$(CC) $(MYCFLAGS) -c defs.c
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#A+++alignmm.o : SA+++alignmm.c $(HEADER)
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# $(CC) $(MYCFLAGS) -c SA+++alignmm.c -o A+++alignmm.o
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Salignmm.o : Salignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Salignmm.c
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Halignmm.o : Halignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Halignmm.c
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Ralignmm.o : Ralignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Ralignmm.c
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Qalignmm.o : Qalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Qalignmm.c
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MSalignmm.o : MSalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c MSalignmm.c
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partSalignmm.o : partSalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c partSalignmm.c
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partQalignmm.o : partQalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c partQalignmm.c
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Lalign11.o : Lalign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Lalign11.c
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genalign11.o : genalign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c genalign11.c
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genGalign11.o : genGalign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c genGalign11.c
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suboptalign11.o : suboptalign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c suboptalign11.c
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Galign11.o : Galign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Galign11.c
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MSalign11.o : MSalign11.c $(HEADER)
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$(CC) $(MYCFLAGS) -c MSalign11.c
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SAalignmm.o : SAalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o
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Lalignmm.o : Lalignmm.c $(HEADER)
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$(CC) $(MYCFLAGS) -c Lalignmm.c
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rna.o : rna.c $(HEADER)
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$(CC) $(MYCFLAGS) -c rna.c
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disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c disttbfast.c
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splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c splitfromaln.c
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splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c splittbfast.c
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splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c splittbfast2.c
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makedirectionlist.o : makedirectionlist.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c makedirectionlist.c
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disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c disttbfast_dummy.c
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dummy.o : dummy.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c dummy.c
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tbfast.o : tbfast.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c tbfast.c
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addsingle.o : addsingle.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c addsingle.c
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tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c tbfast2.c
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setcore.o : setcore.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c setcore.c
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getlag.o : getlag.c $(HEADER) $(FFTHEADER)
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$(CC) $(MYCFLAGS) -c getlag.c
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tditr.o : tditr.c $(HEADER)
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$(CC) $(MYCFLAGS) -c tditr.c
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dvtditr.o : dvtditr.c $(HEADER)
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$(CC) $(MYCFLAGS) -c dvtditr.c
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tditeration.o : tditeration.c $(HEADER)
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$(CC) $(MYCFLAGS) -c tditeration.c
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mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c mafft-profile.c
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dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c dndfast4.c
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dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c dndfast5.c
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dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c dndfast6.c
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dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c dndfast7.c
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dndblast.o : dndblast.c $(HEADER) $(MTXHEADER)
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$(CC) $(MYCFLAGS) -c dndblast.c
423
dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER)
424
$(CC) $(MYCFLAGS) -c dndfast3.c
426
dndpre.o : dndpre.c $(HEADER)
427
$(CC) $(MYCFLAGS) -c dndpre.c
429
countlen.o : countlen.c $(HEADER)
430
$(CC) $(MYCFLAGS) -c countlen.c
432
seq2regtable.o : seq2regtable.c $(HEADER)
433
$(CC) $(MYCFLAGS) -c seq2regtable.c
435
regtable2seq.o : regtable2seq.c $(HEADER)
436
$(CC) $(MYCFLAGS) -c regtable2seq.c
438
f2cl.o : f2cl.c $(HEADER)
439
$(CC) $(MYCFLAGS) -c f2cl.c
441
setdirection.o : setdirection.c $(HEADER)
442
$(CC) $(MYCFLAGS) -c setdirection.c
444
replaceu.o : replaceu.c $(HEADER)
445
$(CC) $(MYCFLAGS) -c replaceu.c
447
restoreu.o : restoreu.c $(HEADER)
448
$(CC) $(MYCFLAGS) -c restoreu.c
450
mccaskillwrap.o : mccaskillwrap.c $(HEADER)
451
$(CC) $(MYCFLAGS) -c mccaskillwrap.c
453
contrafoldwrap.o : contrafoldwrap.c $(HEADER)
454
$(CC) $(MYCFLAGS) -c contrafoldwrap.c
456
pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER)
457
$(CC) $(MYCFLAGS) -c pairlocalalign.c
459
pairash.o : pairash.c $(HEADER) $(FFTHEADER)
460
$(CC) $(MYCFLAGS) -c pairash.c
462
rnatest.o : rnatest.c $(HEADER) $(FFTHEADER)
463
$(CC) $(MYCFLAGS) -c rnatest.c
465
multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
466
$(CC) $(MYCFLAGS) -c multi2hat3s.c
468
pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
469
$(CC) $(MYCFLAGS) -c pair2hat3s.c
471
dndpre2.o : dndpre2.c $(HEADER)
472
$(CC) $(MYCFLAGS) -c dndpre2.c
474
io.o : io.c $(HEADER) $(FFTHEADER)
475
$(CC) $(MYCFLAGS) -c io.c
477
nj.o : nj.c $(HEADER)
478
$(CC) $(MYCFLAGS) -c nj.c
480
treeOperation.o : treeOperation.c $(HEADER)
481
$(CC) $(MYCFLAGS) -c treeOperation.c
483
sextet5.o : sextet5.c $(HEADER) $(MTXHEADER)
484
$(CC) $(MYCFLAGS) -c sextet5.c
486
mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER)
487
$(CC) $(MYCFLAGS) -c mafft-distance.c
489
triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
490
$(CC) $(MYCFLAGS) -c triplet5.c
492
triplet6.o : triplet6.c $(HEADER) $(MTXHEADER)
493
$(CC) $(MYCFLAGS) -c triplet6.c
495
fft.o : fft.c $(HEADER) $(FFTHEADER)
496
$(CC) $(MYCFLAGS) -c fft.c
498
fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER)
499
$(CC) $(MYCFLAGS) -c fftFunctions.c
501
Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
502
$(CC) $(MYCFLAGS) -c Falign.c
504
Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
505
$(CC) $(MYCFLAGS) -c Falign_localhom.c
508
$(CC) $(MYCFLAGS) -c mtxutl.c
510
addfunctions.o : addfunctions.c $(HEADER)
511
$(CC) $(MYCFLAGS) -c addfunctions.c
513
score.o : score.c $(HEADER)
514
$(CC) $(MYCFLAGS) -c score.c
517
rm -f *.o *.a *.exe *~ $(PROGS) $(SCRIPTS)
518
# rm -f ../binaries/* ../scripts/*
526
$(INSTALL) $(SCRIPTS) $(BINDIR)
528
$(INSTALL) -s $(PROGS) $(LIBDIR)
531
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
532
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
533
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
534
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
536
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
537
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
538
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
539
rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
540
rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
added
removed
GDE/MAFFT/mafft-7.055-with-extensions/core/Makefile
