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add package to the repository

msa


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/04/2015 00:12:33
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+# Makefile.in generated by automake 1.10.2 from Makefile.am.
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+# @configure_input@
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+
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+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
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+# 2003, 2004, 2005, 2006, 2007, 2008  Free Software Foundation, Inc.
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+# This Makefile.in is free software; the Free Software Foundation
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+# gives unlimited permission to copy and/or distribute it,
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+# with or without modifications, as long as this notice is preserved.
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+
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+# This program is distributed in the hope that it will be useful,
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+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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+# PARTICULAR PURPOSE.
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+
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+@SET_MAKE@
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+LTLIBRARIES = $(lib_LTLIBRARIES)
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+libclustalo_la_DEPENDENCIES = exceptions4c/libexceptions4c.la clustal/libclustal.la \
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+	hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la argtable2/libargtable2.la
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+am_libclustalo_la_OBJECTS = clustal-omega.lo
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+	--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
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+	$(LDFLAGS) -o $@
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+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
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+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
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+LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
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+	--mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
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+	--mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
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+	$(LDFLAGS) -o $@
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+SOURCES = $(libclustalo_la_SOURCES) $(clustalo_SOURCES)
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+DIST_SOURCES = $(libclustalo_la_SOURCES) $(clustalo_SOURCES)
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+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
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+	html-recursive info-recursive install-data-recursive \
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+	install-dvi-recursive install-exec-recursive \
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+	install-html-recursive install-info-recursive \
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+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
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+  distclean-recursive maintainer-clean-recursive
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+sysconfdir = @sysconfdir@
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+target_alias = @target_alias@
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+top_build_prefix = @top_build_prefix@
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+top_builddir = @top_builddir@
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+top_srcdir = @top_srcdir@
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+EXTRA_DIST = clustalo-api-test.c
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+SUBDIRS = exceptions4c hhalign squid kmpp argtable2 clustal
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+
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+# the following is the clustalo convenience library which wraps all
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+# the other noinst libraries
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+lib_LTLIBRARIES = libclustalo.la
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+libclustalo_la_SOURCES = clustal-omega.c
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+libclustalo_la_LIBADD = exceptions4c/libexceptions4c.la \
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+	clustal/libclustal.la \
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+	hhalign/libhhalign.la \
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+	squid/libsquid.la	\
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+	kmpp/libkmpp.la \
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+	argtable2/libargtable2.la
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+
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+libclustalo_la_LDFLAGS = -static
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+library_includedir = $(includedir)/clustalo/
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+library_include_HEADERS = clustal-omega-config.h clustal-omega.h
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+clustalo_SOURCES = main.cpp \
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+	mymain.c mymain.h
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+
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+clustalo_LDADD = libclustalo.la
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+all: config.h
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+	$(MAKE) $(AM_MAKEFLAGS) all-recursive
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+
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+.SUFFIXES:
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+.SUFFIXES: .c .cpp .lo .o .obj
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+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
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+	@for dep in $?; do \
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+	  case '$(am__configure_deps)' in \
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+	    *$$dep*) \
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+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
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+	        && { if test -f $@; then exit 0; else break; fi; }; \
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+	      exit 1;; \
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+	  esac; \
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+	done; \
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+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu  src/Makefile'; \
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+	cd $(top_srcdir) && \
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+	  $(AUTOMAKE) --gnu  src/Makefile
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+.PRECIOUS: Makefile
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+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
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+	@case '$?' in \
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+	  *config.status*) \
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+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
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+	  *) \
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+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
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+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
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+
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+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
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+$(top_srcdir)/configure:  $(am__configure_deps)
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+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
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+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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+
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+	  rm -f stamp-h1; \
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+	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
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+	else :; fi
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+
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+	cd $(top_srcdir) && $(AUTOHEADER)
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+	rm -f stamp-h1
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+	touch $@
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+
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+distclean-hdr:
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+	-rm -f config.h stamp-h1
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+install-libLTLIBRARIES: $(lib_LTLIBRARIES)
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+	@$(NORMAL_INSTALL)
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+	test -z "$(libdir)" || $(MKDIR_P) "$(DESTDIR)$(libdir)"
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+	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
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+	  if test -f $$p; then \
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+	    f=$(am__strip_dir) \
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+	    echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
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+	    $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \
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+	  else :; fi; \
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+	done
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+
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+uninstall-libLTLIBRARIES:
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+	@$(NORMAL_UNINSTALL)
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+	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
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+	  p=$(am__strip_dir) \
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+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \
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+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \
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+	done
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+
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+clean-libLTLIBRARIES:
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+	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
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+	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
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+	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
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+	  test "$$dir" != "$$p" || dir=.; \
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+	  echo "rm -f \"$${dir}/so_locations\""; \
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+	  rm -f "$${dir}/so_locations"; \
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+	done
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+libclustalo.la: $(libclustalo_la_OBJECTS) $(libclustalo_la_DEPENDENCIES) 
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+	$(libclustalo_la_LINK) -rpath $(libdir) $(libclustalo_la_OBJECTS) $(libclustalo_la_LIBADD) $(LIBS)
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+install-binPROGRAMS: $(bin_PROGRAMS)
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+	@$(NORMAL_INSTALL)
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+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
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+	@list='$(bin_PROGRAMS)'; for p in $$list; do \
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+	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
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+	  if test -f $$p \
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+	     || test -f $$p1 \
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+	  ; then \
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+	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
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+	   echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
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+	   $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
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+	  else :; fi; \
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+	done
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+
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+uninstall-binPROGRAMS:
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+	@$(NORMAL_UNINSTALL)
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+	@list='$(bin_PROGRAMS)'; for p in $$list; do \
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+	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
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+	  echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
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+	  rm -f "$(DESTDIR)$(bindir)/$$f"; \
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+	done
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+
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+clean-binPROGRAMS:
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+	@list='$(bin_PROGRAMS)'; for p in $$list; do \
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+	  f=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
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+	  echo " rm -f $$p $$f"; \
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+	  rm -f $$p $$f ; \
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+	done
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+clustalo$(EXEEXT): $(clustalo_OBJECTS) $(clustalo_DEPENDENCIES) 
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+	@rm -f clustalo$(EXEEXT)
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+	$(CXXLINK) $(clustalo_OBJECTS) $(clustalo_LDADD) $(LIBS)
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+
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+mostlyclean-compile:
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+	-rm -f *.$(OBJEXT)
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+
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+distclean-compile:
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+	-rm -f *.tab.c
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+
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/clustal-omega.Plo@am__quote@
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
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+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mymain.Po@am__quote@
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+
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+.c.o:
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+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
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+@am__fastdepCC_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
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+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
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+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+@am__fastdepCC_FALSE@	$(COMPILE) -c $<
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+
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+.c.obj:
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+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
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+@am__fastdepCC_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
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+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
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+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+@am__fastdepCC_FALSE@	$(COMPILE) -c `$(CYGPATH_W) '$<'`
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+
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+.c.lo:
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+@am__fastdepCC_TRUE@	$(LTCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
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+@am__fastdepCC_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
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+
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