+++ /dev/null
-PREFIX = /usr/local
-LIBDIR = $(PREFIX)/libexec/mafft
-BINDIR = $(PREFIX)/bin
-MANDIR = $(PREFIX)/share/man/man1
-
-#MNO_CYGWIN = -mno-cygwin
-
-#ENABLE_MULTITHREAD = -Denablemultithread
-#Uncomment this to enable multithreading (linux only)
-
-CC = gcc
-CFLAGS = -O3
-#CFLAGS = -O0 -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
-
-MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
-
-ifeq ($(ENABLE_MULTITHREAD),-Denablemultithread)
-LIBS = -lm -lpthread
-else
-LIBS = -lm
-endif
-
-INSTALL = install
-
-PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
- pair2hat3s multi2hat3s rnatest pairash \
- splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
- seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu
-SCRIPTS = mafft mafft-homologs.rb
-OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o
-OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o
-OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.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
-OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
-OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
- multi2hat3s.o defs.o fft.o fftFunctions.o
-OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
- pair2hat3s.o defs.o fft.o fftFunctions.o
-OBJRNATEST = mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o \
- rna.o rnatest.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
- pairash.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
- pairlocalalign.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.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 partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
- Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
- Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
- Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
- Lalign11.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
- disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
- tbfast.o defs.o fft.o fftFunctions.o addfunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
- tbfast2.o defs.o fft.o fftFunctions.o
-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 \
- Falign.o Falign_localhom.o Galign11.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 partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
- Falign.o Falign_localhom.o Galign11.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 partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
- Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \
- tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o
-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 \
- Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.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
-OBJDNDFAST7 = dndfast7.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
-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
-OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.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
-OBJDNDPRESCORE = dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o
-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 \
- SAalignmm.o Galign11.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
-
-HEADER = mltaln.h mtxutl.h
-FFTHEADER = fft.h
-
-MANPAGES = mafft.1 mafft-homologs.1
-
-
-
-all : $(PROGS) $(SCRIPTS)
- cp $(SCRIPTS) ../scripts
- chmod 755 ../scripts/*
- cp $(PROGS) ../binaries
- chmod 755 ../binaries/*
- cp $(MANPAGES) ../binaries
- @echo done.
-
-univscript: univscript.tmpl Makefile
- sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
-
-mafft: mafft.tmpl
- 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
-
-mltaln.h : functions.h
- touch mltaln.h
-
-tbfast : $(OBJTBFAST)
- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
-
-tbfast2 : $(OBJTBFAST2)
- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
-
-disttbfast : $(OBJDISTTBFAST)
- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
-
-splittbfast : $(OBJSPLITTBFAST)
- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
-
-splitfromaln : $(OBJSPLITFROMALN)
- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
-
-splittbfast2 : $(OBJSPLITTBFAST2)
- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
-
-dummy : $(OBJDUMMY)
- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
-
-setcore : $(OBJSETCORE)
- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
-
-countlen : $(OBJCOUNTLEN)
- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
-
-seq2regtable : $(OBJSEQ2REGTABLE)
- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
-
-regtable2seq : $(OBJREGTABLE2SEQ)
- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
-
-replaceu : $(OBJREPLACEU)
- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
-
-restoreu : $(OBJRESTOREU)
- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
-
-f2cl : $(OBJF2CL)
- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
-
-mccaskillwrap : $(OBJMCCASKILLWRAP)
- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
-
-contrafoldwrap : $(OBJCONTRAFOLDWRAP)
- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
-
-pairlocalalign : $(OBJPAIRLOCALALIGN)
- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
-
-pairash : $(OBJPAIRASH)
- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
-
-rnatest : $(OBJRNATEST)
- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
-
-pair2hat3s : $(OBJPAIR2HAT3S)
- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
-
-multi2hat3s : $(OBJMULTI2HAT3S)
- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
-
-getlag : $(OBJGETLAG)
- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
-
-tditr : $(OBJTDITR)
- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
-
-dvtditr : $(OBJDVTDITR)
- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
-
-mafft-profile : $(OBJGALN)
- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
-
-gapfill : $(OBJGAPFILL)
- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
-
-dndfast4 : $(OBJDNDFAST4)
- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
-
-dndfast5 : $(OBJDNDFAST5)
- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
-
-dndfast6 : $(OBJDNDFAST6)
- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
-
-dndfast7 : $(OBJDNDFAST7)
- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
-
-dndblast : $(OBJDNDBLAST)
- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
-
-dndfast3 : $(OBJDNDFAST3)
- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
-
-triplet : $(OBJTRIPLET)
- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
-
-triplet3 : $(OBJTRIPLET3)
- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
-
-sextet3 : $(OBJSEXTET3)
- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
-
-sextet4 : $(OBJSEXTET4)
- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
-
-sextet5 : $(OBJSEXTET5)
- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
-
-mafft-distance : $(OBJDISTANCE)
- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
-
-triplet5 : $(OBJTRIPLET5)
- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
-
-triplet6 : $(OBJTRIPLET6)
- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
-
-octet4 : $(OBJOCTET4)
- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
-
-dndpre : $(OBJDNDPRE)
- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
-
-dndpre2 : $(OBJDNDPRESCORE)
- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
-
-score : $(OBJSCORE)
- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
-
-genMtx : $(OBJGENMTX)
- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
-
-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
-
-Halignmm.o : Halignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c Halignmm.c
-
-Ralignmm.o : Ralignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c Ralignmm.c
-
-Qalignmm.o : Qalignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c Qalignmm.c
-
-MSalignmm.o : MSalignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c MSalignmm.c
-
-partSalignmm.o : partSalignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c partSalignmm.c
-
-partQalignmm.o : partQalignmm.c $(HEADER)
- $(CC) $(MYCFLAGS) -c partQalignmm.c
-
-Lalign11.o : Lalign11.c $(HEADER)
- $(CC) $(MYCFLAGS) -c Lalign11.c
-
-genalign11.o : genalign11.c $(HEADER)
- $(CC) $(MYCFLAGS) -c genalign11.c
-
-genGalign11.o : genGalign11.c $(HEADER)
- $(CC) $(MYCFLAGS) -c genGalign11.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
-
-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
-
-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
-
-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
-
-pairash.o : pairash.c $(HEADER) $(FFTHEADER)
- $(CC) $(MYCFLAGS) -c pairash.c
-
-rnatest.o : rnatest.c $(HEADER) $(FFTHEADER)
- $(CC) $(MYCFLAGS) -c rnatest.c
-
-multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
- $(CC) $(MYCFLAGS) -c multi2hat3s.c
-
-pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
- $(CC) $(MYCFLAGS) -c pair2hat3s.c
-
-dndpre2.o : dndpre2.c $(HEADER)
- $(CC) $(MYCFLAGS) -c dndpre2.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
-
-triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
- $(CC) $(MYCFLAGS) -c triplet5.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 *~ $(PROGS) $(SCRIPTS)
-# rm -f ../binaries/* ../scripts/*
-
-install : all
- mkdir -p $(LIBDIR)
- chmod 755 $(LIBDIR)
- mkdir -p $(BINDIR)
- chmod 755 $(BINDIR)
- chmod 755 $(SCRIPTS)
- $(INSTALL) $(SCRIPTS) $(BINDIR)
- chmod 755 $(PROGS)
- $(INSTALL) $(PROGS) $(LIBDIR)
- $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR)
-
- ( cd $(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; \
-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 $(MANDIR)
- chmod 755 $(MANDIR)
- $(INSTALL) -m 644 $(MANPAGES) $(MANDIR)
-# remove incorrectly installed manpages by previous versions
-# rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1
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