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diff mafft/core/Makefile @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/Makefile	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,551 @@
+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).
+
+CC = gcc
+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
+
+
+MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
+
+ifdef ENABLE_MULTITHREAD
+LIBS = -lm  -lpthread
+else
+LIBS = -lm
+endif
+
+INSTALL = install
+
+PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
+		pair2hat3s multi2hat3s pairash addsingle \
+        splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
+		seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version
+SOS = libdisttbfast.so
+DLLS = libdisttbfast.dll
+DYLIBS = libdisttbfast.dylib
+
+PERLPROGS = mafftash_premafft.pl seekquencer_premafft.pl
+SCRIPTS = mafft mafft-homologs.rb
+OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o
+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
+OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \
+			 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.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 partSalignmm.o Lalignmm.o rna.o Salignmm.o \
+		            Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.o  \
+		    Falign.o Falign_localhom.o Galign11.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  \
+		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+			Lalign11.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 \
+		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+			tbfast.o defs.o fft.o fftFunctions.o addfunctions.o
+OBJADDSINGLE = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+			addsingle.o defs.o fft.o fftFunctions.o addfunctions.o
+OBJTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.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 partSalignmm.o Lalignmm.o rna.o Salignmm.o  \
+			Falign.o Falign_localhom.o Galign11.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 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
+OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.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 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 : $(DLLS)
+
+univscript: univscript.tmpl Makefile
+	sed "s:_PROGS:$(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)
+
+tbfast : $(OBJTBFAST)
+	$(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
+
+addsingle : $(OBJADDSINGLE)
+	$(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
+
+tbfast2 : $(OBJTBFAST2)
+	$(CC) -o $@ $(OBJTBFAST2) $(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)
+
+splittbfast2 : $(OBJSPLITTBFAST2)
+	$(CC) -o $@ $(OBJSPLITTBFAST2) $(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)
+
+pair2hat3s : $(OBJPAIR2HAT3S)
+	$(CC) -o $@ $(OBJPAIR2HAT3S) $(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 
+
+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
+
+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
+
+pairash.o : pairash.c $(HEADER) $(FFTHEADER)
+	$(CC) $(MYCFLAGS) -c pairash.c
+
+multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
+	$(CC) $(MYCFLAGS) -c multi2hat3s.c
+
+pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
+	$(CC) $(MYCFLAGS) -c pair2hat3s.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 *~ $(PERLPROGS) $(PROGS) $(SCRIPTS) $(SOS) $(DYLIBS) $(DLLS) *.gcda *.gcno
+#	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)
+	$(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