PREFIX = /usr/local LIBDIR = $(PREFIX)/libexec/mafft BINDIR = $(PREFIX)/bin MANDIR = $(PREFIX)/share/man/man1 DESTDIR = #MNO_CYGWIN = -mno-cygwin ENABLE_MULTITHREAD = -Denablemultithread # Comment out the above line if your compiler # does not support TLS (thread-local strage). #ENABLE_ATOMIC = -Denableatomic # Comment out the above line if your compiler # does not support "atomic_int". #DASH_CLIENT = dash_client # Uncomment the above line to use protein 3D # structural information. Go language is required. CC = gcc #CC = icc CFLAGS = -O3 #CFLAGS = -O3 -fPIC # add -fPIC when building .so files #CC = icc #CFLAGS = -fast # if you have icc, use this. #CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 #CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 -fprofile-arcs -ftest-coverage #CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind #CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 -lprofiler # ? ifdef ENABLE_MULTITHREAD LIBS = -lm -lpthread else LIBS = -lm endif ifdef ENABLE_ATOMIC STDF = -std=c11 else STDF = -std=c99 endif MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS) INSTALL = install STRIP = strip #STRIP = true # to disable strip PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ multi2hat3s pairash addsingle maffttext2hex hex2maffttext \ splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \ seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version \ $(DASH_CLIENT) SOS = libdisttbfast.so DLLS = libdisttbfast.dll DYLIBS = libdisttbfast.dylib PERLPROGS = mafftash_premafft.pl seekquencer_premafft.pl SCRIPTS = mafft mafft-homologs.rb mafft-sparsecore.rb OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \ multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o \ pairash.o defs.o fft.o fftFunctions.o OBJPAIRLOCALALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o \ pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o OBJDUMMY = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o OBJSPLITFROMALN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ splitfromaln.o defs.o fft.o fftFunctions.o OBJSPLITTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ splittbfast.o defs.o fft.o fftFunctions.o OBJSPLITTBFASTP = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ defs.o fft.o fftFunctions.o OBJDISTTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o OBJMAKEDIRECTIONLIST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o OBJTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \ tbfast.o defs.o fft.o fftFunctions.o addfunctions.o \ pairlocalalign.o MSalign11.o OBJNODPAIR = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \ nodepair.o defs.o fft.o fftFunctions.o addfunctions.o \ pairlocalalign.o MSalign11.o OBJADDSINGLE = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \ addsingle.o defs.o fft.o fftFunctions.o addfunctions.o OBJSETCORE = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \ setcore.o defs.o fft.o fftFunctions.o OBJTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o fftFunctions.o fft.o \ tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o OBJDVTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o \ tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o OBJGETLAG = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o \ getlag.o defs.o fft.o fftFunctions.o OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \ SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o HEADER = mltaln.h mtxutl.h mafft.h FFTHEADER = fft.h MANPAGES = mafft.1 mafft-homologs.1 all : $(PERLPROGS) $(PROGS) $(SCRIPTS) cp $(SCRIPTS) ../scripts chmod 755 ../scripts/* cp $(PERLPROGS) $(PROGS) ../binaries chmod 755 ../binaries/* cp $(MANPAGES) ../binaries @echo done. sos : $(SOS) dylibs : $(DYLIBS) dlls : $(DLLS) $(DASH_CLIENT): dash_client.go go build dash_client.go # go build --ldflags '-extldflags "-static"' dash_client.go univscript: univscript.tmpl Makefile sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript mafft: mafft.tmpl mltaln.h sed "s:_LIBDIR:$(LIBDIR):" mafft.tmpl > mafft mafft-homologs.rb: mafft-homologs.tmpl # cp mafft-homologs.tmpl mafft-homologs.rb sed "s:_BINDIR:$(BINDIR):" mafft-homologs.tmpl > mafft-homologs.rb mafft-sparsecore.rb: mafft-sparsecore.tmpl # cp mafft-sparsecore.tmpl mafft-sparsecore.rb sed "s:_BINDIR:$(BINDIR):" mafft-sparsecore.tmpl > mafft-sparsecore.rb mltaln.h : functions.h touch mltaln.h version : version.c mltaln.h $(CC) -o $@ version.c $(MYCFLAGS) $(LDFLAGS) $(LIBS) maffttext2hex : maffttext2hex.c $(CC) -o $@ maffttext2hex.c $(MYCFLAGS) $(LDFLAGS) $(LIBS) hex2maffttext : hex2maffttext.c $(CC) -o $@ hex2maffttext.c $(MYCFLAGS) $(LDFLAGS) $(LIBS) tbfast : $(OBJTBFAST) $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) nodepair : $(OBJNODPAIR) $(CC) -o $@ $(OBJNODPAIR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) addsingle : $(OBJADDSINGLE) $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) disttbfast : $(OBJDISTTBFAST) $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) libdisttbfast.so : $(OBJDISTTBFAST) $(CC) -shared -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) libdisttbfast.dylib : $(OBJDISTTBFAST) $(CC) -dynamiclib -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) libdisttbfast.dll : $(OBJDISTTBFAST) $(CC) -shared -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) makedirectionlist : $(OBJMAKEDIRECTIONLIST) $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) splittbfast : $(OBJSPLITTBFAST) $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) splitfromaln : $(OBJSPLITFROMALN) $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dummy : $(OBJDUMMY) $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LDFLAGS) $(LIBS) setcore : $(OBJSETCORE) $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) countlen : $(OBJCOUNTLEN) $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) seq2regtable : $(OBJSEQ2REGTABLE) $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) regtable2seq : $(OBJREGTABLE2SEQ) $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LDFLAGS) $(LIBS) setdirection : $(OBJSETDIRECTION) $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LDFLAGS) $(LIBS) replaceu : $(OBJREPLACEU) $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) restoreu : $(OBJRESTOREU) $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) f2cl : $(OBJF2CL) $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) mccaskillwrap : $(OBJMCCASKILLWRAP) $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) contrafoldwrap : $(OBJCONTRAFOLDWRAP) $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) pairlocalalign : $(OBJPAIRLOCALALIGN) $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) pairash : $(OBJPAIRASH) $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LDFLAGS) $(LIBS) multi2hat3s : $(OBJMULTI2HAT3S) $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LDFLAGS) $(LIBS) getlag : $(OBJGETLAG) $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LDFLAGS) $(LIBS) tditr : $(OBJTDITR) $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dvtditr : $(OBJDVTDITR) $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) mafft-profile : $(OBJGALN) $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) gapfill : $(OBJGAPFILL) $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndfast4 : $(OBJDNDFAST4) $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndfast5 : $(OBJDNDFAST5) $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndfast6 : $(OBJDNDFAST6) $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndfast7 : $(OBJDNDFAST7) $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndblast : $(OBJDNDBLAST) $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndfast3 : $(OBJDNDFAST3) $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) triplet : $(OBJTRIPLET) $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LDFLAGS) $(LIBS) triplet3 : $(OBJTRIPLET3) $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) sextet3 : $(OBJSEXTET3) $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) sextet4 : $(OBJSEXTET4) $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) sextet5 : $(OBJSEXTET5) $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) mafft-distance : $(OBJDISTANCE) $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) triplet5 : $(OBJTRIPLET5) $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) triplet6 : $(OBJTRIPLET6) $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) octet4 : $(OBJOCTET4) $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) dndpre : $(OBJDNDPRE) $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) score : $(OBJSCORE) $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) genMtx : $(OBJGENMTX) $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LDFLAGS) $(LIBS) mafftash_premafft.pl : mafftash_premafft.tmpl cp mafftash_premafft.tmpl mafftash_premafft.pl seekquencer_premafft.pl : seekquencer_premafft.tmpl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gapfill.o : gapfill.c $(HEADER) $(CC) $(MYCFLAGS) -c gapfill.c mltaln9.o : mltaln9.c $(HEADER) $(CC) $(MYCFLAGS) -c mltaln9.c tddis.o : tddis.c $(HEADER) $(CC) $(MYCFLAGS) -c tddis.c constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER) $(CC) $(MYCFLAGS) -c constants.c defs.o : defs.c $(CC) $(MYCFLAGS) -c defs.c #A+++alignmm.o : SA+++alignmm.c $(HEADER) # $(CC) $(MYCFLAGS) -c SA+++alignmm.c -o A+++alignmm.o Salignmm.o : Salignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c Salignmm.c Dalignmm.o : Dalignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c Dalignmm.c MSalignmm.o : MSalignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c MSalignmm.c partSalignmm.o : partSalignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c partSalignmm.c Lalign11.o : Lalign11.c $(HEADER) $(CC) $(MYCFLAGS) -c Lalign11.c genalign11.o : genalign11.c $(HEADER) $(CC) $(MYCFLAGS) -c genalign11.c suboptalign11.o : suboptalign11.c $(HEADER) $(CC) $(MYCFLAGS) -c suboptalign11.c Galign11.o : Galign11.c $(HEADER) $(CC) $(MYCFLAGS) -c Galign11.c MSalign11.o : MSalign11.c $(HEADER) $(CC) $(MYCFLAGS) -c MSalign11.c SAalignmm.o : SAalignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o Lalignmm.o : Lalignmm.c $(HEADER) $(CC) $(MYCFLAGS) -c Lalignmm.c rna.o : rna.c $(HEADER) $(CC) $(MYCFLAGS) -c rna.c disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c disttbfast.c splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c splitfromaln.c splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c splittbfast.c splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c splittbfast2.c makedirectionlist.o : makedirectionlist.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c makedirectionlist.c disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c disttbfast_dummy.c dummy.o : dummy.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c dummy.c tbfast.o : tbfast.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c tbfast.c nodepair.o : nodepair.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c nodepair.c addsingle.o : addsingle.c $(HEADER) $(FFTHEADER) addsingle.o : addsingle.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c addsingle.c tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c tbfast2.c setcore.o : setcore.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c setcore.c getlag.o : getlag.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c getlag.c tditr.o : tditr.c $(HEADER) $(CC) $(MYCFLAGS) -c tditr.c dvtditr.o : dvtditr.c $(HEADER) $(CC) $(MYCFLAGS) -c dvtditr.c tditeration.o : tditeration.c $(HEADER) $(CC) $(MYCFLAGS) -c tditeration.c mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c mafft-profile.c dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndfast4.c dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndfast5.c dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndfast6.c dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndfast7.c dndblast.o : dndblast.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndblast.c dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c dndfast3.c dndpre.o : dndpre.c $(HEADER) $(CC) $(MYCFLAGS) -c dndpre.c countlen.o : countlen.c $(HEADER) $(CC) $(MYCFLAGS) -c countlen.c seq2regtable.o : seq2regtable.c $(HEADER) $(CC) $(MYCFLAGS) -c seq2regtable.c regtable2seq.o : regtable2seq.c $(HEADER) $(CC) $(MYCFLAGS) -c regtable2seq.c f2cl.o : f2cl.c $(HEADER) $(CC) $(MYCFLAGS) -c f2cl.c setdirection.o : setdirection.c $(HEADER) $(CC) $(MYCFLAGS) -c setdirection.c replaceu.o : replaceu.c $(HEADER) $(CC) $(MYCFLAGS) -c replaceu.c restoreu.o : restoreu.c $(HEADER) $(CC) $(MYCFLAGS) -c restoreu.c mccaskillwrap.o : mccaskillwrap.c $(HEADER) $(CC) $(MYCFLAGS) -c mccaskillwrap.c contrafoldwrap.o : contrafoldwrap.c $(HEADER) $(CC) $(MYCFLAGS) -c contrafoldwrap.c pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c pairlocalalign.c pairlocalalignmain.o : pairlocalalignmain.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c pairlocalalignmain.c pairash.o : pairash.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c pairash.c multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c multi2hat3s.c io.o : io.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c io.c nj.o : nj.c $(HEADER) $(CC) $(MYCFLAGS) -c nj.c treeOperation.o : treeOperation.c $(HEADER) $(CC) $(MYCFLAGS) -c treeOperation.c sextet5.o : sextet5.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c sextet5.c mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c mafft-distance.c maffttext2hex.o : maffttext2hex.c $(CC) $(MYCFLAGS) -c maffttext2hex.c hex2maffttext.o : hex2maffttext.c $(CC) $(MYCFLAGS) -c hex2maffttext.c triplet6.o : triplet6.c $(HEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c triplet6.c fft.o : fft.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c fft.c fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER) $(CC) $(MYCFLAGS) -c fftFunctions.c Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c Falign.c Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER) $(CC) $(MYCFLAGS) -c Falign_localhom.c mtxutl.o : mtxutl.c $(CC) $(MYCFLAGS) -c mtxutl.c addfunctions.o : addfunctions.c $(HEADER) $(CC) $(MYCFLAGS) -c addfunctions.c score.o : score.c $(HEADER) $(CC) $(MYCFLAGS) -c score.c clean : rm -f *.o *.a *.exe *~ $(PERLPROGS) $(PROGS) $(SCRIPTS) $(SOS) $(DYLIBS) $(DLLS) *.gcda *.gcno $(DASH_CLIENT) # rm -f ../binaries/* ../scripts/* install : all mkdir -p $(DESTDIR)$(LIBDIR) chmod 755 $(DESTDIR)$(LIBDIR) mkdir -p $(DESTDIR)$(BINDIR) chmod 755 $(DESTDIR)$(BINDIR) chmod 755 $(SCRIPTS) $(INSTALL) $(SCRIPTS) $(DESTDIR)$(BINDIR) chmod 755 $(PROGS) ||: # in MinGW, it's ok if this fails # $(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR) $(STRIP) $(PROGS) ||: # may fail for dash_client on mac. $(INSTALL) $(PROGS) $(DESTDIR)$(LIBDIR) $(INSTALL) $(PERLPROGS) $(DESTDIR)$(LIBDIR) $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(LIBDIR) ( cd $(DESTDIR)$(BINDIR); \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . ) mkdir -p $(DESTDIR)$(MANDIR) chmod 755 $(DESTDIR)$(MANDIR) $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(MANDIR) # remove incorrectly installed manpages by previous versions # rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1