2 LIBDIR = $(PREFIX)/libexec/mafft
4 MANDIR = $(PREFIX)/share/man/man1
6 #MNO_CYGWIN = -mno-cygwin
8 #ENABLE_MULTITHREAD = -Denablemultithread
9 #Uncomment this to enable multithreading (linux only)
13 #CFLAGS = -O0 -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
15 MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
17 ifeq ($(ENABLE_MULTITHREAD),-Denablemultithread)
25 PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
26 pair2hat3s multi2hat3s rnatest pairash \
27 splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
28 seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu
29 SCRIPTS = mafft mafft-homologs.rb
30 OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o
31 OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o
32 OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o
33 OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o
34 OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o
35 OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o
36 OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
37 OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
38 OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
39 multi2hat3s.o defs.o fft.o fftFunctions.o
40 OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
41 pair2hat3s.o defs.o fft.o fftFunctions.o
42 OBJRNATEST = mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o \
43 rna.o rnatest.o defs.o fft.o fftFunctions.o
44 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 \
45 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
46 pairash.o defs.o fft.o fftFunctions.o
47 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 \
48 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
49 pairlocalalign.o defs.o fft.o fftFunctions.o
50 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 \
51 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
52 disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o
53 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 \
54 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
55 Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
56 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 \
57 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
58 Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o
59 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 \
60 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
61 Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
62 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 \
63 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
64 Lalign11.o defs.o fft.o fftFunctions.o
65 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 \
66 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
67 disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o
68 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 \
69 Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
70 tbfast.o defs.o fft.o fftFunctions.o addfunctions.o
71 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 \
72 Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
73 tbfast2.o defs.o fft.o fftFunctions.o
74 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 \
75 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
76 setcore.o defs.o fft.o fftFunctions.o
77 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 \
78 Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o \
79 tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o
80 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 \
81 Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \
82 tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o
83 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 \
84 Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
85 getlag.o defs.o fft.o fftFunctions.o
86 OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o
87 OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
88 OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
89 OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
90 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
91 OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
92 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
93 OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
94 OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o
95 OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o
96 OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o
97 OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o
98 OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o
99 OBJDNDPRESCORE = dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o
100 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 \
101 SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
102 OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o
104 HEADER = mltaln.h mtxutl.h
107 MANPAGES = mafft.1 mafft-homologs.1
111 all : $(PROGS) $(SCRIPTS)
112 cp $(SCRIPTS) ../scripts
113 chmod 755 ../scripts/*
114 cp $(PROGS) ../binaries
115 chmod 755 ../binaries/*
116 cp $(MANPAGES) ../binaries
119 univscript: univscript.tmpl Makefile
120 sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
123 sed "s:_LIBDIR:$(LIBDIR):" mafft.tmpl > mafft
125 mafft-homologs.rb: mafft-homologs.tmpl
126 # cp mafft-homologs.tmpl mafft-homologs.rb
127 sed "s:_BINDIR:$(BINDIR):" mafft-homologs.tmpl > mafft-homologs.rb
129 mltaln.h : functions.h
132 tbfast : $(OBJTBFAST)
133 $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
135 tbfast2 : $(OBJTBFAST2)
136 $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
138 disttbfast : $(OBJDISTTBFAST)
139 $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
141 splittbfast : $(OBJSPLITTBFAST)
142 $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
144 splitfromaln : $(OBJSPLITFROMALN)
145 $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
147 splittbfast2 : $(OBJSPLITTBFAST2)
148 $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
151 $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
153 setcore : $(OBJSETCORE)
154 $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
156 countlen : $(OBJCOUNTLEN)
157 $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
159 seq2regtable : $(OBJSEQ2REGTABLE)
160 $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
162 regtable2seq : $(OBJREGTABLE2SEQ)
163 $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
165 replaceu : $(OBJREPLACEU)
166 $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
168 restoreu : $(OBJRESTOREU)
169 $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
172 $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
174 mccaskillwrap : $(OBJMCCASKILLWRAP)
175 $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
177 contrafoldwrap : $(OBJCONTRAFOLDWRAP)
178 $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
180 pairlocalalign : $(OBJPAIRLOCALALIGN)
181 $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
183 pairash : $(OBJPAIRASH)
184 $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
186 rnatest : $(OBJRNATEST)
187 $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
189 pair2hat3s : $(OBJPAIR2HAT3S)
190 $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
192 multi2hat3s : $(OBJMULTI2HAT3S)
193 $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
195 getlag : $(OBJGETLAG)
196 $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
199 $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
201 dvtditr : $(OBJDVTDITR)
202 $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
204 mafft-profile : $(OBJGALN)
205 $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
207 gapfill : $(OBJGAPFILL)
208 $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
210 dndfast4 : $(OBJDNDFAST4)
211 $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
213 dndfast5 : $(OBJDNDFAST5)
214 $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
216 dndfast6 : $(OBJDNDFAST6)
217 $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
219 dndfast7 : $(OBJDNDFAST7)
220 $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
222 dndblast : $(OBJDNDBLAST)
223 $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
225 dndfast3 : $(OBJDNDFAST3)
226 $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
228 triplet : $(OBJTRIPLET)
229 $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
231 triplet3 : $(OBJTRIPLET3)
232 $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
234 sextet3 : $(OBJSEXTET3)
235 $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
237 sextet4 : $(OBJSEXTET4)
238 $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
240 sextet5 : $(OBJSEXTET5)
241 $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
243 mafft-distance : $(OBJDISTANCE)
244 $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
246 triplet5 : $(OBJTRIPLET5)
247 $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
249 triplet6 : $(OBJTRIPLET6)
250 $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
252 octet4 : $(OBJOCTET4)
253 $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
255 dndpre : $(OBJDNDPRE)
256 $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
258 dndpre2 : $(OBJDNDPRESCORE)
259 $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
262 $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
264 genMtx : $(OBJGENMTX)
265 $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
267 gapfill.o : gapfill.c $(HEADER)
268 $(CC) $(MYCFLAGS) -c gapfill.c
270 mltaln9.o : mltaln9.c $(HEADER)
271 $(CC) $(MYCFLAGS) -c mltaln9.c
273 tddis.o : tddis.c $(HEADER)
274 $(CC) $(MYCFLAGS) -c tddis.c
276 constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER)
277 $(CC) $(MYCFLAGS) -c constants.c
280 $(CC) $(MYCFLAGS) -c defs.c
282 #A+++alignmm.o : SA+++alignmm.c $(HEADER)
283 # $(CC) $(MYCFLAGS) -c SA+++alignmm.c -o A+++alignmm.o
285 Salignmm.o : Salignmm.c $(HEADER)
286 $(CC) $(MYCFLAGS) -c Salignmm.c
288 Halignmm.o : Halignmm.c $(HEADER)
289 $(CC) $(MYCFLAGS) -c Halignmm.c
291 Ralignmm.o : Ralignmm.c $(HEADER)
292 $(CC) $(MYCFLAGS) -c Ralignmm.c
294 Qalignmm.o : Qalignmm.c $(HEADER)
295 $(CC) $(MYCFLAGS) -c Qalignmm.c
297 MSalignmm.o : MSalignmm.c $(HEADER)
298 $(CC) $(MYCFLAGS) -c MSalignmm.c
300 partSalignmm.o : partSalignmm.c $(HEADER)
301 $(CC) $(MYCFLAGS) -c partSalignmm.c
303 partQalignmm.o : partQalignmm.c $(HEADER)
304 $(CC) $(MYCFLAGS) -c partQalignmm.c
306 Lalign11.o : Lalign11.c $(HEADER)
307 $(CC) $(MYCFLAGS) -c Lalign11.c
309 genalign11.o : genalign11.c $(HEADER)
310 $(CC) $(MYCFLAGS) -c genalign11.c
312 genGalign11.o : genGalign11.c $(HEADER)
313 $(CC) $(MYCFLAGS) -c genGalign11.c
315 suboptalign11.o : suboptalign11.c $(HEADER)
316 $(CC) $(MYCFLAGS) -c suboptalign11.c
318 Galign11.o : Galign11.c $(HEADER)
319 $(CC) $(MYCFLAGS) -c Galign11.c
321 MSalign11.o : MSalign11.c $(HEADER)
322 $(CC) $(MYCFLAGS) -c MSalign11.c
324 SAalignmm.o : SAalignmm.c $(HEADER)
325 $(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o
327 Lalignmm.o : Lalignmm.c $(HEADER)
328 $(CC) $(MYCFLAGS) -c Lalignmm.c
330 rna.o : rna.c $(HEADER)
331 $(CC) $(MYCFLAGS) -c rna.c
333 disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER)
334 $(CC) $(MYCFLAGS) -c disttbfast.c
336 splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER)
337 $(CC) $(MYCFLAGS) -c splitfromaln.c
339 splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER)
340 $(CC) $(MYCFLAGS) -c splittbfast.c
342 splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER)
343 $(CC) $(MYCFLAGS) -c splittbfast2.c
345 disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER)
346 $(CC) $(MYCFLAGS) -c disttbfast_dummy.c
348 dummy.o : dummy.c $(HEADER) $(FFTHEADER)
349 $(CC) $(MYCFLAGS) -c dummy.c
351 tbfast.o : tbfast.c $(HEADER) $(FFTHEADER)
352 $(CC) $(MYCFLAGS) -c tbfast.c
354 tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER)
355 $(CC) $(MYCFLAGS) -c tbfast2.c
357 setcore.o : setcore.c $(HEADER) $(FFTHEADER)
358 $(CC) $(MYCFLAGS) -c setcore.c
360 getlag.o : getlag.c $(HEADER) $(FFTHEADER)
361 $(CC) $(MYCFLAGS) -c getlag.c
363 tditr.o : tditr.c $(HEADER)
364 $(CC) $(MYCFLAGS) -c tditr.c
366 dvtditr.o : dvtditr.c $(HEADER)
367 $(CC) $(MYCFLAGS) -c dvtditr.c
369 tditeration.o : tditeration.c $(HEADER)
370 $(CC) $(MYCFLAGS) -c tditeration.c
372 mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER)
373 $(CC) $(MYCFLAGS) -c mafft-profile.c
375 dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER)
376 $(CC) $(MYCFLAGS) -c dndfast4.c
378 dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER)
379 $(CC) $(MYCFLAGS) -c dndfast5.c
381 dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER)
382 $(CC) $(MYCFLAGS) -c dndfast6.c
384 dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER)
385 $(CC) $(MYCFLAGS) -c dndfast7.c
387 dndblast.o : dndblast.c $(HEADER) $(MTXHEADER)
388 $(CC) $(MYCFLAGS) -c dndblast.c
390 dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER)
391 $(CC) $(MYCFLAGS) -c dndfast3.c
393 dndpre.o : dndpre.c $(HEADER)
394 $(CC) $(MYCFLAGS) -c dndpre.c
396 countlen.o : countlen.c $(HEADER)
397 $(CC) $(MYCFLAGS) -c countlen.c
399 seq2regtable.o : seq2regtable.c $(HEADER)
400 $(CC) $(MYCFLAGS) -c seq2regtable.c
402 regtable2seq.o : regtable2seq.c $(HEADER)
403 $(CC) $(MYCFLAGS) -c regtable2seq.c
405 f2cl.o : f2cl.c $(HEADER)
406 $(CC) $(MYCFLAGS) -c f2cl.c
408 replaceu.o : replaceu.c $(HEADER)
409 $(CC) $(MYCFLAGS) -c replaceu.c
411 restoreu.o : restoreu.c $(HEADER)
412 $(CC) $(MYCFLAGS) -c restoreu.c
414 mccaskillwrap.o : mccaskillwrap.c $(HEADER)
415 $(CC) $(MYCFLAGS) -c mccaskillwrap.c
417 contrafoldwrap.o : contrafoldwrap.c $(HEADER)
418 $(CC) $(MYCFLAGS) -c contrafoldwrap.c
420 pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER)
421 $(CC) $(MYCFLAGS) -c pairlocalalign.c
423 pairash.o : pairash.c $(HEADER) $(FFTHEADER)
424 $(CC) $(MYCFLAGS) -c pairash.c
426 rnatest.o : rnatest.c $(HEADER) $(FFTHEADER)
427 $(CC) $(MYCFLAGS) -c rnatest.c
429 multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
430 $(CC) $(MYCFLAGS) -c multi2hat3s.c
432 pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
433 $(CC) $(MYCFLAGS) -c pair2hat3s.c
435 dndpre2.o : dndpre2.c $(HEADER)
436 $(CC) $(MYCFLAGS) -c dndpre2.c
438 io.o : io.c $(HEADER) $(FFTHEADER)
439 $(CC) $(MYCFLAGS) -c io.c
441 nj.o : nj.c $(HEADER)
442 $(CC) $(MYCFLAGS) -c nj.c
444 treeOperation.o : treeOperation.c $(HEADER)
445 $(CC) $(MYCFLAGS) -c treeOperation.c
447 sextet5.o : sextet5.c $(HEADER) $(MTXHEADER)
448 $(CC) $(MYCFLAGS) -c sextet5.c
450 mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER)
451 $(CC) $(MYCFLAGS) -c mafft-distance.c
453 triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
454 $(CC) $(MYCFLAGS) -c triplet5.c
456 triplet6.o : triplet6.c $(HEADER) $(MTXHEADER)
457 $(CC) $(MYCFLAGS) -c triplet6.c
459 fft.o : fft.c $(HEADER) $(FFTHEADER)
460 $(CC) $(MYCFLAGS) -c fft.c
462 fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER)
463 $(CC) $(MYCFLAGS) -c fftFunctions.c
465 Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
466 $(CC) $(MYCFLAGS) -c Falign.c
468 Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
469 $(CC) $(MYCFLAGS) -c Falign_localhom.c
472 $(CC) $(MYCFLAGS) -c mtxutl.c
474 addfunctions.o : addfunctions.c $(HEADER)
475 $(CC) $(MYCFLAGS) -c addfunctions.c
477 score.o : score.c $(HEADER)
478 $(CC) $(MYCFLAGS) -c score.c
481 rm -f *.o *.a *.exe *~ $(PROGS) $(SCRIPTS)
482 # rm -f ../binaries/* ../scripts/*
490 $(INSTALL) $(SCRIPTS) $(BINDIR)
492 $(INSTALL) $(PROGS) $(LIBDIR)
493 $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR)
496 rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
497 rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
498 ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
499 ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
501 ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
502 ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
503 ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
504 rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
505 rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
509 $(INSTALL) -m 644 $(MANPAGES) $(MANDIR)
510 # remove incorrectly installed manpages by previous versions
511 # rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1