2 LIBDIR = $(PREFIX)/lib/mafft
4 MANDIR = $(PREFIX)/man/man1
6 #MNO_CYGWIN = -mno-cygwin
10 CFLAGS = -O0 -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
11 #CFLAGS = -O3 $(MNO_CYGWIN)
12 #CFLAGS = -mno-cygwin -O3 # for cygwin
13 #CFLAGS = -fast -static # for icc on Intel
14 #CFLAGS = -O3 -ipo -static # for icc on AMD
17 #CFLAGS = -ansi -pedantic
22 PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
23 pair2hat3s multi2hat3s rnatest pairash \
24 splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
25 seq2regtable regtable2seq score getlag dndpre dndpre2 setcore
26 SCRIPTS = mafft mafft-homologs.rb
27 OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o
28 OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o
29 OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o
30 OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o
31 OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
32 OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
33 OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
34 multi2hat3s.o defs.o fft.o fftFunctions.o
35 OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
36 pair2hat3s.o defs.o fft.o fftFunctions.o
37 OBJRNATEST = mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o \
38 rna.o rnatest.o defs.o fft.o fftFunctions.o
39 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 \
40 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
41 Calignm1.o pairash.o defs.o fft.o fftFunctions.o
42 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 \
43 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
44 Calignm1.o pairlocalalign.o defs.o fft.o fftFunctions.o
45 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 \
46 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
47 disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o
48 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 \
49 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
50 Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
51 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 \
52 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
53 Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o
54 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 \
55 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
56 Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
57 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 \
58 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
59 Lalign11.o defs.o fft.o fftFunctions.o
60 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 \
61 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
62 disttbfast.o defs.o fft.o fftFunctions.o
63 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 \
64 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o \
65 tbfast.o defs.o fft.o fftFunctions.o
66 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 \
67 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o \
68 tbfast2.o defs.o fft.o fftFunctions.o
69 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 \
70 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
71 setcore.o defs.o fft.o fftFunctions.o
72 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 \
73 Calignm1.o Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o \
74 tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o
75 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 \
76 Calignm1.o Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \
77 tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o
78 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 \
79 Falign.o Falign_localhom.o Galign11.o SAalignmm.o Calignm1.o MSalignmm.o \
80 getlag.o defs.o fft.o fftFunctions.o
81 OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o
82 OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
83 OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
84 OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
85 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
86 OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
87 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
88 OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
89 OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o
90 OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o
91 OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o
92 OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o
93 OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o
94 OBJDNDPRESCORE = dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o
95 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 \
96 Calignm1.o SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
97 OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o
99 HEADER = mltaln.h mtxutl.h
103 MANPAGES = mafft.1 mafft-homologs.1
107 all : $(PROGS) $(SCRIPTS)
108 cp $(SCRIPTS) ../scripts
109 chmod 755 ../scripts/*
110 cp $(PROGS) $(MANPAGES) ../binaries
111 chmod 755 ../binaries/*
114 univscript: univscript.tmpl Makefile
115 sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
118 sed "s:_LIBDIR:$(LIBDIR):" mafft.tmpl > mafft
120 mafft-homologs.rb: mafft-homologs.tmpl
121 # cp mafft-homologs.tmpl mafft-homologs.rb
122 sed "s:_BINDIR:$(BINDIR):" mafft-homologs.tmpl > mafft-homologs.rb
124 mltaln.h : functions.h
128 $(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
130 tbfast : $(OBJTBFAST)
131 $(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
133 tbfast2 : $(OBJTBFAST2)
134 $(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
136 disttbfast : $(OBJDISTTBFAST)
137 $(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
139 splittbfast : $(OBJSPLITTBFAST)
140 $(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
142 splitfromaln : $(OBJSPLITFROMALN)
143 $(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
145 splittbfast2 : $(OBJSPLITTBFAST2)
146 $(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
149 $(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
151 setcore : $(OBJSETCORE)
152 $(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
154 countlen : $(OBJCOUNTLEN)
155 $(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
157 seq2regtable : $(OBJSEQ2REGTABLE)
158 $(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
160 regtable2seq : $(OBJREGTABLE2SEQ)
161 $(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
164 $(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
166 mccaskillwrap : $(OBJMCCASKILLWRAP)
167 $(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
169 contrafoldwrap : $(OBJCONTRAFOLDWRAP)
170 $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
172 pairlocalalign : $(OBJPAIRLOCALALIGN)
173 $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
175 pairash : $(OBJPAIRASH)
176 $(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
178 rnatest : $(OBJRNATEST)
179 $(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
181 pair2hat3s : $(OBJPAIR2HAT3S)
182 $(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
184 multi2hat3s : $(OBJMULTI2HAT3S)
185 $(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
187 getlag : $(OBJGETLAG)
188 $(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
191 $(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
193 dvtditr : $(OBJDVTDITR)
194 $(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
196 mafft-profile : $(OBJGALN)
197 $(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
199 gapfill : $(OBJGAPFILL)
200 $(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
202 dndfast4 : $(OBJDNDFAST4)
203 $(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
205 dndfast5 : $(OBJDNDFAST5)
206 $(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
208 dndfast6 : $(OBJDNDFAST6)
209 $(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
211 dndfast7 : $(OBJDNDFAST7)
212 $(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
214 dndblast : $(OBJDNDBLAST)
215 $(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
217 dndfast3 : $(OBJDNDFAST3)
218 $(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
220 triplet : $(OBJTRIPLET)
221 $(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
223 triplet3 : $(OBJTRIPLET3)
224 $(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
226 sextet3 : $(OBJSEXTET3)
227 $(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
229 sextet4 : $(OBJSEXTET4)
230 $(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
232 sextet5 : $(OBJSEXTET5)
233 $(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
235 mafft-distance : $(OBJDISTANCE)
236 $(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
238 triplet5 : $(OBJTRIPLET5)
239 $(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
241 triplet6 : $(OBJTRIPLET6)
242 $(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
244 octet4 : $(OBJOCTET4)
245 $(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
247 dndpre : $(OBJDNDPRE)
248 $(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
250 dndpre2 : $(OBJDNDPRESCORE)
251 $(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
254 $(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
256 genMtx : $(OBJGENMTX)
257 $(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
259 gapfill.o : gapfill.c $(HEADER)
260 $(CC) $(CFLAGS) -c gapfill.c
262 mltaln9.o : mltaln9.c $(HEADER)
263 $(CC) $(CFLAGS) -c mltaln9.c
265 tddis.o : tddis.c $(HEADER)
266 $(CC) $(CFLAGS) -c tddis.c
268 constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER)
269 $(CC) $(CFLAGS) -c constants.c
272 $(CC) $(CFLAGS) -c defs.c
274 Calignm1.o : Calignm1.c $(HEADER) $(DPHEADER)
275 $(CC) $(CFLAGS) -c Calignm1.c
277 #A+++alignmm.o : SA+++alignmm.c $(HEADER) $(DPHEADER)
278 # $(CC) $(CFLAGS) -c SA+++alignmm.c -o A+++alignmm.o
280 Salignmm.o : Salignmm.c $(HEADER) $(DPHEADER)
281 $(CC) $(CFLAGS) -c Salignmm.c
283 Halignmm.o : Halignmm.c $(HEADER) $(DPHEADER)
284 $(CC) $(CFLAGS) -c Halignmm.c
286 Ralignmm.o : Ralignmm.c $(HEADER) $(DPHEADER)
287 $(CC) $(CFLAGS) -c Ralignmm.c
289 Qalignmm.o : Qalignmm.c $(HEADER) $(DPHEADER)
290 $(CC) $(CFLAGS) -c Qalignmm.c
292 MSalignmm.o : MSalignmm.c $(HEADER) $(DPHEADER)
293 $(CC) $(CFLAGS) -c MSalignmm.c
295 partSalignmm.o : partSalignmm.c $(HEADER) $(DPHEADER)
296 $(CC) $(CFLAGS) -c partSalignmm.c
298 partQalignmm.o : partQalignmm.c $(HEADER) $(DPHEADER)
299 $(CC) $(CFLAGS) -c partQalignmm.c
301 Lalign11.o : Lalign11.c $(HEADER) $(DPHEADER)
302 $(CC) $(CFLAGS) -c Lalign11.c
304 genalign11.o : genalign11.c $(HEADER) $(DPHEADER)
305 $(CC) $(CFLAGS) -c genalign11.c
307 genGalign11.o : genGalign11.c $(HEADER) $(DPHEADER)
308 $(CC) $(CFLAGS) -c genGalign11.c
310 suboptalign11.o : suboptalign11.c $(HEADER) $(DPHEADER)
311 $(CC) $(CFLAGS) -c suboptalign11.c
313 Galign11.o : Galign11.c $(HEADER) $(DPHEADER)
314 $(CC) $(CFLAGS) -c Galign11.c
316 MSalign11.o : MSalign11.c $(HEADER) $(DPHEADER)
317 $(CC) $(CFLAGS) -c MSalign11.c
319 SAalignmm.o : SAalignmm.c $(HEADER) $(DPHEADER)
320 $(CC) $(CFLAGS) -c SAalignmm.c -o SAalignmm.o
322 Lalignmm.o : Lalignmm.c $(HEADER) $(DPHEADER)
323 $(CC) $(CFLAGS) -c Lalignmm.c
325 rna.o : rna.c $(HEADER) $(DPHEADER)
326 $(CC) $(CFLAGS) -c rna.c
328 ord.o : ord.c $(HEADER)
329 $(CC) $(CFLAGS) -c ord.c
331 1itr.o : 1itr.c $(HEADER)
332 $(CC) $(CFLAGS) -c 1itr.c
334 tb.o : tb.c $(HEADER)
335 $(CC) $(CFLAGS) -c tb.c
337 disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER)
338 $(CC) $(CFLAGS) -c disttbfast.c
340 splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER)
341 $(CC) $(CFLAGS) -c splitfromaln.c
343 splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER)
344 $(CC) $(CFLAGS) -c splittbfast.c
346 splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER)
347 $(CC) $(CFLAGS) -c splittbfast2.c
349 disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER)
350 $(CC) $(CFLAGS) -c disttbfast_dummy.c
352 dummy.o : dummy.c $(HEADER) $(FFTHEADER)
353 $(CC) $(CFLAGS) -c dummy.c
355 tbfast.o : tbfast.c $(HEADER) $(FFTHEADER)
356 $(CC) $(CFLAGS) -c tbfast.c
358 tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER)
359 $(CC) $(CFLAGS) -c tbfast2.c
361 setcore.o : setcore.c $(HEADER) $(FFTHEADER)
362 $(CC) $(CFLAGS) -c setcore.c
364 getlag.o : getlag.c $(HEADER) $(FFTHEADER)
365 $(CC) $(CFLAGS) -c getlag.c
367 tditr.o : tditr.c $(HEADER)
368 $(CC) $(CFLAGS) -c tditr.c
370 dvtditr.o : dvtditr.c $(HEADER)
371 $(CC) $(CFLAGS) -c dvtditr.c
373 tditeration.o : tditeration.c $(HEADER)
374 $(CC) $(CFLAGS) -c tditeration.c
376 mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER)
377 $(CC) $(CFLAGS) -c mafft-profile.c
379 dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER)
380 $(CC) $(CFLAGS) -c dndfast4.c
382 dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER)
383 $(CC) $(CFLAGS) -c dndfast5.c
385 dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER)
386 $(CC) $(CFLAGS) -c dndfast6.c
388 dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER)
389 $(CC) $(CFLAGS) -c dndfast7.c
391 dndblast.o : dndblast.c $(HEADER) $(MTXHEADER)
392 $(CC) $(CFLAGS) -c dndblast.c
394 dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER)
395 $(CC) $(CFLAGS) -c dndfast3.c
397 dndpre.o : dndpre.c $(HEADER)
398 $(CC) $(CFLAGS) -c dndpre.c
400 countlen.o : countlen.c $(HEADER)
401 $(CC) $(CFLAGS) -c countlen.c
403 seq2regtable.o : seq2regtable.c $(HEADER)
404 $(CC) $(CFLAGS) -c seq2regtable.c
406 regtable2seq.o : regtable2seq.c $(HEADER)
407 $(CC) $(CFLAGS) -c regtable2seq.c
409 f2cl.o : f2cl.c $(HEADER)
410 $(CC) $(CFLAGS) -c f2cl.c
412 mccaskillwrap.o : mccaskillwrap.c $(HEADER)
413 $(CC) $(CFLAGS) -c mccaskillwrap.c
415 contrafoldwrap.o : contrafoldwrap.c $(HEADER)
416 $(CC) $(CFLAGS) -c contrafoldwrap.c
418 pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER)
419 $(CC) $(CFLAGS) -c pairlocalalign.c
421 pairash.o : pairash.c $(HEADER) $(FFTHEADER)
422 $(CC) $(CFLAGS) -c pairash.c
424 rnatest.o : rnatest.c $(HEADER) $(FFTHEADER)
425 $(CC) $(CFLAGS) -c rnatest.c
427 multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
428 $(CC) $(CFLAGS) -c multi2hat3s.c
430 pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
431 $(CC) $(CFLAGS) -c pair2hat3s.c
433 dndpre2.o : dndpre2.c $(HEADER)
434 $(CC) $(CFLAGS) -c dndpre2.c
436 io.o : io.c $(HEADER) $(FFTHEADER)
437 $(CC) $(CFLAGS) -c io.c
439 nj.o : nj.c $(HEADER)
440 $(CC) $(CFLAGS) -c nj.c
442 treeOperation.o : treeOperation.c $(HEADER)
443 $(CC) $(CFLAGS) -c treeOperation.c
445 sextet5.o : sextet5.c $(HEADER) $(MTXHEADER)
446 $(CC) $(CFLAGS) -c sextet5.c
448 mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER)
449 $(CC) $(CFLAGS) -c mafft-distance.c
451 triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
452 $(CC) $(CFLAGS) -c triplet5.c
454 triplet6.o : triplet6.c $(HEADER) $(MTXHEADER)
455 $(CC) $(CFLAGS) -c triplet6.c
457 fft.o : fft.c $(HEADER) $(FFTHEADER)
458 $(CC) $(CFLAGS) -c fft.c
460 fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER)
461 $(CC) $(CFLAGS) -c fftFunctions.c
463 Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
464 $(CC) $(CFLAGS) -c Falign.c
466 Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
467 $(CC) $(CFLAGS) -c Falign_localhom.c
470 $(CC) $(CFLAGS) -c mtxutl.c
472 score.o : score.c $(HEADER)
473 $(CC) $(CFLAGS) -c score.c
476 rm -f *.o *.a *.exe *~ $(PROGS) $(SCRIPTS)
477 # rm -f ../binaries/* ../scripts/*
485 $(INSTALL) $(SCRIPTS) $(BINDIR)
487 $(INSTALL) $(PROGS) $(MANPAGES) $(LIBDIR)
489 rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
490 rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
491 ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
492 ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
494 ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
495 ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
496 ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
497 rm -f mafft-profile mafft-profile.exe; ln -s ../lib/mafft/mafft-profile .; \
498 rm -f mafft-distance mafft-distance.exe; ln -s ../lib/mafft/mafft-distance . )
502 $(INSTALL) $(MANPAGES) $(MANDIR)