1PREFIX = /usr/local 2LIBDIR = $(PREFIX)/libexec/mafft 3BINDIR = $(PREFIX)/bin 4MANDIR = $(PREFIX)/share/man/man1 5 6#MNO_CYGWIN = -mno-cygwin 7 8ENABLE_MULTITHREAD = -Denablemultithread 9# Comment out the above line if your compiler 10# does not support TLS (thread-local strage). 11 12CC = gcc 13#CFLAGS = -O3 14#CFLAGS = -O3 -fPIC 15# add -fPIC when building .so files 16 17#CC = icc 18#CFLAGS = -fast 19# if you have icc, use this. 20 21#CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 22CFLAGS = -fPIC -O0 -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind 23 24 25MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS) 26 27ifdef ENABLE_MULTITHREAD 28LIBS = -lm -lpthread 29else 30LIBS = -lm 31endif 32 33INSTALL = install 34 35PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ 36 pair2hat3s multi2hat3s pairash addsingle \ 37 splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \ 38 seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version 39SOS = libdisttbfast.so 40DLLS = libdisttbfast.dll 41DYLIBS = libdisttbfast.dylib 42 43PERLPROGS = mafftash_premafft.pl seekquencer_premafft.pl 44SCRIPTS = mafft mafft-homologs.rb 45OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o 46OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o 47OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o 48OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o 49OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o 50OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o 51OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o 52OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o 53OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o 54OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \ 55 multi2hat3s.o defs.o fft.o fftFunctions.o 56OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \ 57 pair2hat3s.o defs.o fft.o fftFunctions.o 58OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 59 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o \ 60 pairash.o defs.o fft.o fftFunctions.o 61OBJPAIRLOCALALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 62 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o \ 63 pairlocalalign.o defs.o fft.o fftFunctions.o 64OBJDUMMY = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 65 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 66 disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o 67OBJSPLITFROMALN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 68 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 69 Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o 70OBJSPLITTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 71 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 72 Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o 73OBJSPLITTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 74 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 75 Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o 76OBJSPLITTBFASTP = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 77 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 78 Lalign11.o defs.o fft.o fftFunctions.o 79OBJDISTTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 80 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 81 disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o 82OBJMAKEDIRECTIONLIST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 83 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 84 Lalign11.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o 85OBJTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 86 Falign.o Falign_localhom.o Galign11.o SAalignmm.o \ 87 tbfast.o defs.o fft.o fftFunctions.o addfunctions.o 88OBJADDSINGLE = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 89 Falign.o Falign_localhom.o Galign11.o SAalignmm.o \ 90 addsingle.o defs.o fft.o fftFunctions.o addfunctions.o 91OBJTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o MSalignmm.o \ 92 Falign.o Falign_localhom.o Galign11.o SAalignmm.o \ 93 tbfast2.o defs.o fft.o fftFunctions.o 94OBJSETCORE = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 95 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 96 setcore.o defs.o fft.o fftFunctions.o 97OBJTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 98 Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o \ 99 tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o 100OBJDVTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 101 Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \ 102 tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o 103OBJGETLAG = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \ 104 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \ 105 getlag.o defs.o fft.o fftFunctions.o 106OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o 107OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 108OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 109OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 110OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 111OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 112OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o 113OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o 114OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o 115OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o 116OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o 117OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o 118OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o 119OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o \ 120 SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o 121OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o 122 123HEADER = mltaln.h mtxutl.h mafft.h 124FFTHEADER = fft.h 125 126MANPAGES = mafft.1 mafft-homologs.1 127 128 129 130 131all : $(PERLPROGS) $(PROGS) $(SCRIPTS) 132 cp $(SCRIPTS) ../scripts 133 chmod 755 ../scripts/* 134 cp $(PERLPROGS) $(PROGS) ../binaries 135 chmod 755 ../binaries/* 136 cp $(MANPAGES) ../binaries 137 @echo done. 138 139sos : $(SOS) 140dylibs : $(DYLIBS) 141dlls : $(DLLS) 142 143univscript: univscript.tmpl Makefile 144 sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript 145 146mafft: mafft.tmpl mltaln.h 147 sed "s:_LIBDIR:$(LIBDIR):" mafft.tmpl > mafft 148 149mafft-homologs.rb: mafft-homologs.tmpl 150# cp mafft-homologs.tmpl mafft-homologs.rb 151 sed "s:_BINDIR:$(BINDIR):" mafft-homologs.tmpl > mafft-homologs.rb 152 153mltaln.h : functions.h 154 touch mltaln.h 155 156version : version.c mltaln.h 157 $(CC) -o $@ version.c $(MYCFLAGS) $(LDFLAGS) 158 159tbfast : $(OBJTBFAST) 160 $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 161 162addsingle : $(OBJADDSINGLE) 163 $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 164 165tbfast2 : $(OBJTBFAST2) 166 $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 167 168disttbfast : $(OBJDISTTBFAST) 169 $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 170 171libdisttbfast.so : $(OBJDISTTBFAST) 172 $(CC) -shared -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 173 174libdisttbfast.dylib : $(OBJDISTTBFAST) 175 $(CC) -dynamiclib -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 176 177libdisttbfast.dll : $(OBJDISTTBFAST) 178 $(CC) -shared -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 179 180makedirectionlist : $(OBJMAKEDIRECTIONLIST) 181 $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 182 183splittbfast : $(OBJSPLITTBFAST) 184 $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 185 186splitfromaln : $(OBJSPLITFROMALN) 187 $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 188 189splittbfast2 : $(OBJSPLITTBFAST2) 190 $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 191 192dummy : $(OBJDUMMY) 193 $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 194 195setcore : $(OBJSETCORE) 196 $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 197 198countlen : $(OBJCOUNTLEN) 199 $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 200 201seq2regtable : $(OBJSEQ2REGTABLE) 202 $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 203 204regtable2seq : $(OBJREGTABLE2SEQ) 205 $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 206 207setdirection : $(OBJSETDIRECTION) 208 $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 209 210replaceu : $(OBJREPLACEU) 211 $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 212 213restoreu : $(OBJRESTOREU) 214 $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 215 216f2cl : $(OBJF2CL) 217 $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 218 219mccaskillwrap : $(OBJMCCASKILLWRAP) 220 $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 221 222contrafoldwrap : $(OBJCONTRAFOLDWRAP) 223 $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 224 225pairlocalalign : $(OBJPAIRLOCALALIGN) 226 $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 227 228pairash : $(OBJPAIRASH) 229 $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 230 231pair2hat3s : $(OBJPAIR2HAT3S) 232 $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 233 234multi2hat3s : $(OBJMULTI2HAT3S) 235 $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 236 237getlag : $(OBJGETLAG) 238 $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 239 240tditr : $(OBJTDITR) 241 $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 242 243dvtditr : $(OBJDVTDITR) 244 $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 245 246mafft-profile : $(OBJGALN) 247 $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 248 249gapfill : $(OBJGAPFILL) 250 $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 251 252dndfast4 : $(OBJDNDFAST4) 253 $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 254 255dndfast5 : $(OBJDNDFAST5) 256 $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 257 258dndfast6 : $(OBJDNDFAST6) 259 $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 260 261dndfast7 : $(OBJDNDFAST7) 262 $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 263 264dndblast : $(OBJDNDBLAST) 265 $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 266 267dndfast3 : $(OBJDNDFAST3) 268 $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 269 270triplet : $(OBJTRIPLET) 271 $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 272 273triplet3 : $(OBJTRIPLET3) 274 $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 275 276sextet3 : $(OBJSEXTET3) 277 $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 278 279sextet4 : $(OBJSEXTET4) 280 $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 281 282sextet5 : $(OBJSEXTET5) 283 $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 284 285mafft-distance : $(OBJDISTANCE) 286 $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 287 288triplet5 : $(OBJTRIPLET5) 289 $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 290 291triplet6 : $(OBJTRIPLET6) 292 $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 293 294octet4 : $(OBJOCTET4) 295 $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 296 297dndpre : $(OBJDNDPRE) 298 $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 299 300score : $(OBJSCORE) 301 $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 302 303genMtx : $(OBJGENMTX) 304 $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LDFLAGS) $(LIBS) 305 306mafftash_premafft.pl : mafftash_premafft.tmpl 307 cp mafftash_premafft.tmpl mafftash_premafft.pl 308 309seekquencer_premafft.pl : seekquencer_premafft.tmpl 310 cp seekquencer_premafft.tmpl seekquencer_premafft.pl 311 312gapfill.o : gapfill.c $(HEADER) 313 $(CC) $(MYCFLAGS) -c gapfill.c 314 315mltaln9.o : mltaln9.c $(HEADER) 316 $(CC) $(MYCFLAGS) -c mltaln9.c 317 318tddis.o : tddis.c $(HEADER) 319 $(CC) $(MYCFLAGS) -c tddis.c 320 321constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER) 322 $(CC) $(MYCFLAGS) -c constants.c 323 324defs.o : defs.c 325 $(CC) $(MYCFLAGS) -c defs.c 326 327#A+++alignmm.o : SA+++alignmm.c $(HEADER) 328# $(CC) $(MYCFLAGS) -c SA+++alignmm.c -o A+++alignmm.o 329 330Salignmm.o : Salignmm.c $(HEADER) 331 $(CC) $(MYCFLAGS) -c Salignmm.c 332 333MSalignmm.o : MSalignmm.c $(HEADER) 334 $(CC) $(MYCFLAGS) -c MSalignmm.c 335 336partSalignmm.o : partSalignmm.c $(HEADER) 337 $(CC) $(MYCFLAGS) -c partSalignmm.c 338 339Lalign11.o : Lalign11.c $(HEADER) 340 $(CC) $(MYCFLAGS) -c Lalign11.c 341 342genalign11.o : genalign11.c $(HEADER) 343 $(CC) $(MYCFLAGS) -c genalign11.c 344 345suboptalign11.o : suboptalign11.c $(HEADER) 346 $(CC) $(MYCFLAGS) -c suboptalign11.c 347 348Galign11.o : Galign11.c $(HEADER) 349 $(CC) $(MYCFLAGS) -c Galign11.c 350 351MSalign11.o : MSalign11.c $(HEADER) 352 $(CC) $(MYCFLAGS) -c MSalign11.c 353 354SAalignmm.o : SAalignmm.c $(HEADER) 355 $(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o 356 357Lalignmm.o : Lalignmm.c $(HEADER) 358 $(CC) $(MYCFLAGS) -c Lalignmm.c 359 360rna.o : rna.c $(HEADER) 361 $(CC) $(MYCFLAGS) -c rna.c 362 363disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER) 364 $(CC) $(MYCFLAGS) -c disttbfast.c 365 366splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER) 367 $(CC) $(MYCFLAGS) -c splitfromaln.c 368 369splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER) 370 $(CC) $(MYCFLAGS) -c splittbfast.c 371 372splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER) 373 $(CC) $(MYCFLAGS) -c splittbfast2.c 374 375makedirectionlist.o : makedirectionlist.c $(HEADER) $(FFTHEADER) 376 $(CC) $(MYCFLAGS) -c makedirectionlist.c 377 378disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER) 379 $(CC) $(MYCFLAGS) -c disttbfast_dummy.c 380 381dummy.o : dummy.c $(HEADER) $(FFTHEADER) 382 $(CC) $(MYCFLAGS) -c dummy.c 383 384tbfast.o : tbfast.c $(HEADER) $(FFTHEADER) 385 $(CC) $(MYCFLAGS) -c tbfast.c 386 387addsingle.o : addsingle.c $(HEADER) $(FFTHEADER) 388 $(CC) $(MYCFLAGS) -c addsingle.c 389 390tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER) 391 $(CC) $(MYCFLAGS) -c tbfast2.c 392 393setcore.o : setcore.c $(HEADER) $(FFTHEADER) 394 $(CC) $(MYCFLAGS) -c setcore.c 395 396getlag.o : getlag.c $(HEADER) $(FFTHEADER) 397 $(CC) $(MYCFLAGS) -c getlag.c 398 399tditr.o : tditr.c $(HEADER) 400 $(CC) $(MYCFLAGS) -c tditr.c 401 402dvtditr.o : dvtditr.c $(HEADER) 403 $(CC) $(MYCFLAGS) -c dvtditr.c 404 405tditeration.o : tditeration.c $(HEADER) 406 $(CC) $(MYCFLAGS) -c tditeration.c 407 408mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER) 409 $(CC) $(MYCFLAGS) -c mafft-profile.c 410 411dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER) 412 $(CC) $(MYCFLAGS) -c dndfast4.c 413 414dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER) 415 $(CC) $(MYCFLAGS) -c dndfast5.c 416 417dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER) 418 $(CC) $(MYCFLAGS) -c dndfast6.c 419 420dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER) 421 $(CC) $(MYCFLAGS) -c dndfast7.c 422 423dndblast.o : dndblast.c $(HEADER) $(MTXHEADER) 424 $(CC) $(MYCFLAGS) -c dndblast.c 425 426dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER) 427 $(CC) $(MYCFLAGS) -c dndfast3.c 428 429dndpre.o : dndpre.c $(HEADER) 430 $(CC) $(MYCFLAGS) -c dndpre.c 431 432countlen.o : countlen.c $(HEADER) 433 $(CC) $(MYCFLAGS) -c countlen.c 434 435seq2regtable.o : seq2regtable.c $(HEADER) 436 $(CC) $(MYCFLAGS) -c seq2regtable.c 437 438regtable2seq.o : regtable2seq.c $(HEADER) 439 $(CC) $(MYCFLAGS) -c regtable2seq.c 440 441f2cl.o : f2cl.c $(HEADER) 442 $(CC) $(MYCFLAGS) -c f2cl.c 443 444setdirection.o : setdirection.c $(HEADER) 445 $(CC) $(MYCFLAGS) -c setdirection.c 446 447replaceu.o : replaceu.c $(HEADER) 448 $(CC) $(MYCFLAGS) -c replaceu.c 449 450restoreu.o : restoreu.c $(HEADER) 451 $(CC) $(MYCFLAGS) -c restoreu.c 452 453mccaskillwrap.o : mccaskillwrap.c $(HEADER) 454 $(CC) $(MYCFLAGS) -c mccaskillwrap.c 455 456contrafoldwrap.o : contrafoldwrap.c $(HEADER) 457 $(CC) $(MYCFLAGS) -c contrafoldwrap.c 458 459pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER) 460 $(CC) $(MYCFLAGS) -c pairlocalalign.c 461 462pairash.o : pairash.c $(HEADER) $(FFTHEADER) 463 $(CC) $(MYCFLAGS) -c pairash.c 464 465multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER) 466 $(CC) $(MYCFLAGS) -c multi2hat3s.c 467 468pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER) 469 $(CC) $(MYCFLAGS) -c pair2hat3s.c 470 471io.o : io.c $(HEADER) $(FFTHEADER) 472 $(CC) $(MYCFLAGS) -c io.c 473 474nj.o : nj.c $(HEADER) 475 $(CC) $(MYCFLAGS) -c nj.c 476 477treeOperation.o : treeOperation.c $(HEADER) 478 $(CC) $(MYCFLAGS) -c treeOperation.c 479 480sextet5.o : sextet5.c $(HEADER) $(MTXHEADER) 481 $(CC) $(MYCFLAGS) -c sextet5.c 482 483mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER) 484 $(CC) $(MYCFLAGS) -c mafft-distance.c 485 486triplet5.o : triplet5.c $(HEADER) $(MTXHEADER) 487 $(CC) $(MYCFLAGS) -c triplet5.c 488 489triplet6.o : triplet6.c $(HEADER) $(MTXHEADER) 490 $(CC) $(MYCFLAGS) -c triplet6.c 491 492fft.o : fft.c $(HEADER) $(FFTHEADER) 493 $(CC) $(MYCFLAGS) -c fft.c 494 495fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER) 496 $(CC) $(MYCFLAGS) -c fftFunctions.c 497 498Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER) 499 $(CC) $(MYCFLAGS) -c Falign.c 500 501Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER) 502 $(CC) $(MYCFLAGS) -c Falign_localhom.c 503 504mtxutl.o : mtxutl.c 505 $(CC) $(MYCFLAGS) -c mtxutl.c 506 507addfunctions.o : addfunctions.c $(HEADER) 508 $(CC) $(MYCFLAGS) -c addfunctions.c 509 510score.o : score.c $(HEADER) 511 $(CC) $(MYCFLAGS) -c score.c 512 513clean : 514 rm -f *.o *.a *.exe *~ $(PERLPROGS) $(PROGS) $(SCRIPTS) $(SOS) $(DYLIBS) $(DLLS) 515# rm -f ../binaries/* ../scripts/* 516 517install : all 518 mkdir -p $(LIBDIR) 519 chmod 755 $(LIBDIR) 520 mkdir -p $(BINDIR) 521 chmod 755 $(BINDIR) 522 chmod 755 $(SCRIPTS) 523 $(INSTALL) $(SCRIPTS) $(BINDIR) 524 chmod 755 $(PROGS) 525 $(INSTALL) -s $(PROGS) $(LIBDIR) 526 $(INSTALL) $(PERLPROGS) $(LIBDIR) 527 $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) 528 529 ( cd $(BINDIR); \ 530rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ 531rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \ 532ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ 533ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ 534ln -s mafft einsi; \ 535ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ 536ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ 537ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ 538rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \ 539rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . ) 540 541 mkdir -p $(MANDIR) 542 chmod 755 $(MANDIR) 543 $(INSTALL) -m 644 $(MANPAGES) $(MANDIR) 544# remove incorrectly installed manpages by previous versions 545# rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1 546