Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / Makefile.in

diff --git a/website/archive/binaries/mac/src/clustalw/src/Makefile.in b/website/archive/binaries/mac/src/clustalw/src/Makefile.in
new file mode 100644 (file)
index 0000000..679917c
--- /dev/null
+++ b/website/archive/binaries/mac/src/clustalw/src/Makefile.in
@@ -0,0 +1,1486 @@
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008  Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+# Andreas Wilm (UCD): 2007-12-10
+# Generated using the following sites 
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+target_triplet = @target@
+bin_PROGRAMS = clustalw2$(EXEEXT)
+subdir = src
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+       $(srcdir)/clustalw_version.h.in $(srcdir)/config.h.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+       $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = config.h
+CONFIG_CLEAN_FILES = clustalw_version.h
+am__installdirs = "$(DESTDIR)$(bindir)"
+binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
+PROGRAMS = $(bin_PROGRAMS)
+am_clustalw2_OBJECTS = FullPairwiseAlign.$(OBJEXT) \
+       FastPairwiseAlign.$(OBJEXT) MSFFileParser.$(OBJEXT) \
+       FileReader.$(OBJEXT) PIRFileParser.$(OBJEXT) \
+       RSFFileParser.$(OBJEXT) GDEFileParser.$(OBJEXT) \
+       InFileStream.$(OBJEXT) ClustalFileParser.$(OBJEXT) \
+       PearsonFileParser.$(OBJEXT) FileParser.$(OBJEXT) \
+       EMBLFileParser.$(OBJEXT) RootedClusterTree.$(OBJEXT) \
+       UPGMAAlgorithm.$(OBJEXT) Node.$(OBJEXT) \
+       RootedGuideTree.$(OBJEXT) RootedTreeOutput.$(OBJEXT) \
+       Tree.$(OBJEXT) ClusterTree.$(OBJEXT) TreeInterface.$(OBJEXT) \
+       UnRootedClusterTree.$(OBJEXT) ClusterTreeOutput.$(OBJEXT) \
+       RandomGenerator.$(OBJEXT) NJTree.$(OBJEXT) \
+       AlignmentSteps.$(OBJEXT) InteractiveMenu.$(OBJEXT) \
+       CommandLineParser.$(OBJEXT) SubMatrix.$(OBJEXT) \
+       Iteration.$(OBJEXT) MSA.$(OBJEXT) \
+       MyersMillerProfileAlign.$(OBJEXT) ProfileStandard.$(OBJEXT) \
+       ProfileWithSub.$(OBJEXT) ProfileBase.$(OBJEXT) \
+       LowScoreSegProfile.$(OBJEXT) OutputFile.$(OBJEXT) \
+       UserParameters.$(OBJEXT) Utility.$(OBJEXT) \
+       InvalidCombination.$(OBJEXT) DebugLog.$(OBJEXT) \
+       ClustalWResources.$(OBJEXT) VectorOutOfRange.$(OBJEXT) \
+       SymMatrix.$(OBJEXT) Stats.$(OBJEXT) Help.$(OBJEXT) \
+       Alignment.$(OBJEXT) AlignmentOutput.$(OBJEXT) \
+       ObjectiveScore.$(OBJEXT) Sequence.$(OBJEXT) Clustal.$(OBJEXT) \
+       main.$(OBJEXT)
+clustalw2_OBJECTS = $(am_clustalw2_OBJECTS)
+clustalw2_LDADD = $(LDADD)
+DEFAULT_INCLUDES = -I.@am__isrc@
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+       $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
+       -o $@
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+       $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+SOURCES = $(clustalw2_SOURCES)
+DIST_SOURCES = $(clustalw2_SOURCES)
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+       html-recursive info-recursive install-data-recursive \
+       install-dvi-recursive install-exec-recursive \
+       install-html-recursive install-info-recursive \
+       install-pdf-recursive install-ps-recursive install-recursive \
+       installcheck-recursive installdirs-recursive pdf-recursive \
+       ps-recursive uninstall-recursive
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive        \
+  distclean-recursive maintainer-clean-recursive
+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = $(SUBDIRS)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CLUSTALW_NAME = @CLUSTALW_NAME@
+CLUSTALW_VERSION = @CLUSTALW_VERSION@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GREP = @GREP@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+OBJEXT = @OBJEXT@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+RANLIB = @RANLIB@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target = @target@
+target_alias = @target_alias@
+target_cpu = @target_cpu@
+target_os = @target_os@
+target_vendor = @target_vendor@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+# we do not use GNU-style files: NEWS README AUTHORS ChangeLog
+AUTOMAKE_OPTIONS = foreign
+SUBDIRS = 
+clustalw2_SOURCES = ./pairwise/PairwiseAlignBase.h \
+ ./pairwise/FastPairwiseAlign.h \
+ ./pairwise/FullPairwiseAlign.cpp \
+ ./pairwise/FullPairwiseAlign.h \
+ ./pairwise/FastPairwiseAlign.cpp \
+ ./fileInput/FileParser.h \
+ ./fileInput/EMBLFileParser.h \
+ ./fileInput/MSFFileParser.cpp \
+ ./fileInput/FileReader.cpp \
+ ./fileInput/PIRFileParser.cpp \
+ ./fileInput/MSFFileParser.h \
+ ./fileInput/FileReader.h \
+ ./fileInput/RSFFileParser.cpp \
+ ./fileInput/PIRFileParser.h \
+ ./fileInput/GDEFileParser.cpp \
+ ./fileInput/RSFFileParser.h \
+ ./fileInput/GDEFileParser.h \
+ ./fileInput/InFileStream.cpp \
+ ./fileInput/ClustalFileParser.cpp \
+ ./fileInput/PearsonFileParser.cpp \
+ ./fileInput/InFileStream.h \
+ ./fileInput/ClustalFileParser.h \
+ ./fileInput/PearsonFileParser.h \
+ ./fileInput/FileParser.cpp \
+ ./fileInput/EMBLFileParser.cpp \
+ ./tree/UPGMA/RootedClusterTree.cpp \
+ ./tree/UPGMA/RootedGuideTree.h \
+ ./tree/UPGMA/UPGMAAlgorithm.cpp \
+ ./tree/UPGMA/RootedTreeOutput.h \
+ ./tree/UPGMA/RootedClusterTree.h \
+ ./tree/UPGMA/Node.cpp \
+ ./tree/UPGMA/UPGMAAlgorithm.h \
+ ./tree/UPGMA/upgmadata.h \
+ ./tree/UPGMA/Node.h \
+ ./tree/UPGMA/RootedGuideTree.cpp \
+ ./tree/UPGMA/RootedTreeOutput.cpp \
+ ./tree/Tree.cpp \
+ ./tree/ClusterTree.cpp \
+ ./tree/AlignmentSteps.h \
+ ./tree/Tree.h \
+ ./tree/ClusterTree.h \
+ ./tree/ClusterTreeAlgorithm.h \
+ ./tree/TreeInterface.cpp \
+ ./tree/UnRootedClusterTree.cpp \
+ ./tree/ClusterTreeOutput.cpp \
+ ./tree/TreeInterface.h \
+ ./tree/dayhoff.h \
+ ./tree/UnRootedClusterTree.h \
+ ./tree/RandomGenerator.cpp \
+ ./tree/NJTree.cpp \
+ ./tree/ClusterTreeOutput.h \
+ ./tree/RandomGenerator.h \
+ ./tree/NJTree.h \
+ ./tree/AlignmentSteps.cpp \
+ ./interface/InteractiveMenu.cpp \
+ ./interface/CommandLineParser.cpp \
+ ./interface/InteractiveMenu.h \
+ ./interface/CommandLineParser.h \
+ ./substitutionMatrix/SubMatrix.cpp \
+ ./substitutionMatrix/SubMatrix.h \
+ ./substitutionMatrix/globalmatrix.h \
+ ./substitutionMatrix/matrices.h \
+ ./multipleAlign/Iteration.cpp \
+ ./multipleAlign/MSA.cpp \
+ ./multipleAlign/MyersMillerProfileAlign.cpp \
+ ./multipleAlign/ProfileBase.h \
+ ./multipleAlign/ProfileStandard.cpp \
+ ./multipleAlign/LowScoreSegProfile.h \
+ ./multipleAlign/Iteration.h \
+ ./multipleAlign/MSA.h \
+ ./multipleAlign/MyersMillerProfileAlign.h \
+ ./multipleAlign/ProfileStandard.h \
+ ./multipleAlign/ProfileWithSub.cpp \
+ ./multipleAlign/ProfileAlignAlgorithm.h \
+ ./multipleAlign/ProfileBase.cpp \
+ ./multipleAlign/ProfileWithSub.h \
+ ./multipleAlign/LowScoreSegProfile.cpp \
+ ./general/ClustalWResources.h \
+ ./general/OutputFile.cpp \
+ ./general/VectorOutOfRange.h \
+ ./general/UserParameters.cpp \
+ ./general/SymMatrix.h \
+ ./general/Utility.cpp \
+ ./general/clustalw.h \
+ ./general/OutputFile.h \
+ ./general/param.h \
+ ./general/utils.h \
+ ./general/UserParameters.h \
+ ./general/SquareMat.h \
+ ./general/Utility.h \
+ ./general/SequenceNotFoundException.h \
+ ./general/InvalidCombination.cpp \
+ ./general/Array2D.h \
+ ./general/RandomAccessLList.h \
+ ./general/general.h \
+ ./general/debuglogObject.h \
+ ./general/statsObject.h \
+ ./general/userparams.h \
+ ./general/DebugLog.cpp \
+ ./general/ClustalWResources.cpp \
+ ./general/VectorUtility.h \
+ ./general/VectorOutOfRange.cpp \
+ ./general/SymMatrix.cpp \
+ ./general/DebugLog.h \
+ ./general/Stats.cpp \
+ ./general/Stats.h \
+ ./Help.cpp \
+ ./Help.h \
+ ./alignment/Alignment.cpp \
+ ./alignment/AlignmentOutput.cpp \
+ ./alignment/Alignment.h \
+ ./alignment/AlignmentOutput.h \
+ ./alignment/ObjectiveScore.cpp \
+ ./alignment/Sequence.cpp \
+ ./alignment/ObjectiveScore.h \
+ ./alignment/Sequence.h \
+ ./Clustal.cpp \
+ ./Clustal.h \
+ ./clustalw_version.h \
+ ./main.cpp
+
+all: config.h
+       $(MAKE) $(AM_MAKEFLAGS) all-recursive
+
+.SUFFIXES:
+.SUFFIXES: .cpp .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+       @for dep in $?; do \
+         case '$(am__configure_deps)' in \
+           *$$dep*) \
+             ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+               && { if test -f $@; then exit 0; else break; fi; }; \
+             exit 1;; \
+         esac; \
+       done; \
+       echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  src/Makefile'; \
+       cd $(top_srcdir) && \
+         $(AUTOMAKE) --foreign  src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+       @case '$?' in \
+         *config.status*) \
+           cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+         *) \
+           echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+           cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+       esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+config.h: stamp-h1
+       @if test ! -f $@; then \
+         rm -f stamp-h1; \
+         $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
+       else :; fi
+
+stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
+       @rm -f stamp-h1
+       cd $(top_builddir) && $(SHELL) ./config.status src/config.h
+$(srcdir)/config.h.in:  $(am__configure_deps) 
+       cd $(top_srcdir) && $(AUTOHEADER)
+       rm -f stamp-h1
+       touch $@
+
+distclean-hdr:
+       -rm -f config.h stamp-h1
+clustalw_version.h: $(top_builddir)/config.status $(srcdir)/clustalw_version.h.in
+       cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+install-binPROGRAMS: $(bin_PROGRAMS)
+       @$(NORMAL_INSTALL)
+       test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+       @list='$(bin_PROGRAMS)'; for p in $$list; do \
+         p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
+         if test -f $$p \
+         ; then \
+           f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
+          echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
+          $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
+         else :; fi; \
+       done
+
+uninstall-binPROGRAMS:
+       @$(NORMAL_UNINSTALL)
+       @list='$(bin_PROGRAMS)'; for p in $$list; do \
+         f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
+         echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
+         rm -f "$(DESTDIR)$(bindir)/$$f"; \
+       done
+
+clean-binPROGRAMS:
+       -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+clustalw2$(EXEEXT): $(clustalw2_OBJECTS) $(clustalw2_DEPENDENCIES) 
+       @rm -f clustalw2$(EXEEXT)
+       $(CXXLINK) $(clustalw2_OBJECTS) $(clustalw2_LDADD) $(LIBS)
+
+mostlyclean-compile:
+       -rm -f *.$(OBJEXT)
+
+distclean-compile:
+       -rm -f *.tab.c
+
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Alignment.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/AlignmentOutput.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/AlignmentSteps.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Clustal.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ClustalFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ClustalWResources.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ClusterTree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ClusterTreeOutput.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/CommandLineParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/DebugLog.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/EMBLFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/FastPairwiseAlign.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/FileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/FileReader.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/FullPairwiseAlign.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GDEFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Help.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/InFileStream.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/InteractiveMenu.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/InvalidCombination.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Iteration.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/LowScoreSegProfile.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/MSA.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/MSFFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/MyersMillerProfileAlign.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/NJTree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Node.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ObjectiveScore.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/OutputFile.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/PIRFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/PearsonFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ProfileBase.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ProfileStandard.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ProfileWithSub.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RSFFileParser.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RandomGenerator.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RootedClusterTree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RootedGuideTree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RootedTreeOutput.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Sequence.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Stats.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/SubMatrix.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/SymMatrix.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Tree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/TreeInterface.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/UPGMAAlgorithm.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/UnRootedClusterTree.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/UserParameters.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Utility.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/VectorOutOfRange.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
+
+.cpp.o:
+@am__fastdepCXX_TRUE@  $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
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+TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+               $(TAGS_FILES) $(LISP)
+       tags=; \
+       here=`pwd`; \
+       if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+         include_option=--etags-include; \
+         empty_fix=.; \
+       else \
+         include_option=--include; \
+         empty_fix=; \
+       fi; \
+       list='$(SUBDIRS)'; for subdir in $$list; do \
+         if test "$$subdir" = .; then :; else \
+           test ! -f $$subdir/TAGS || \
+             tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+         fi; \
+       done; \
+       list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+       unique=`for i in $$list; do \
+           if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+         done | \
+         $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+             END { if (nonempty) { for (i in files) print i; }; }'`; \
+       if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+         test -n "$$unique" || unique=$$empty_fix; \
+         $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+           $$tags $$unique; \
+       fi
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+               $(TAGS_FILES) $(LISP)
+       tags=; \
+       list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+       unique=`for i in $$list; do \
+           if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+         done | \
+         $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+             END { if (nonempty) { for (i in files) print i; }; }'`; \
+       test -z "$(CTAGS_ARGS)$$tags$$unique" \
+         || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+            $$tags $$unique
+
+GTAGS:
+       here=`$(am__cd) $(top_builddir) && pwd` \
+         && cd $(top_srcdir) \
+         && gtags -i $(GTAGS_ARGS) $$here
+
+distclean-tags:
+       -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+       @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+       topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+       list='$(DISTFILES)'; \
+         dist_files=`for file in $$list; do echo $$file; done | \
+         sed -e "s|^$$srcdirstrip/||;t" \
+             -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+       case $$dist_files in \
+         */*) $(MKDIR_P) `echo "$$dist_files" | \
+                          sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+                          sort -u` ;; \
+       esac; \
+       for file in $$dist_files; do \
+         if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+         if test -d $$d/$$file; then \
+           dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+           if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+             cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+           fi; \
+           cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+         else \
+           test -f $(distdir)/$$file \
+           || cp -p $$d/$$file $(distdir)/$$file \
+           || exit 1; \
+         fi; \
+       done
+       list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+         if test "$$subdir" = .; then :; else \
+           test -d "$(distdir)/$$subdir" \
+           || $(MKDIR_P) "$(distdir)/$$subdir" \
+           || exit 1; \
+           distdir=`$(am__cd) $(distdir) && pwd`; \
+           top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
+           (cd $$subdir && \
+             $(MAKE) $(AM_MAKEFLAGS) \
+               top_distdir="$$top_distdir" \
+               distdir="$$distdir/$$subdir" \
+               am__remove_distdir=: \
+               am__skip_length_check=: \
+               distdir) \
+             || exit 1; \
+         fi; \
+       done
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(PROGRAMS) config.h
+installdirs: installdirs-recursive
+installdirs-am:
+       for dir in "$(DESTDIR)$(bindir)"; do \
+         test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+       done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+       @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+       $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+         install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+         `test -z '$(STRIP)' || \
+           echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+       -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+       @echo "This command is intended for maintainers to use"
+       @echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-recursive
+       -rm -rf ./$(DEPDIR)
+       -rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+       distclean-hdr distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+info: info-recursive
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-recursive
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-recursive
+
+install-info: install-info-recursive
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-ps: install-ps-recursive
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+       -rm -rf ./$(DEPDIR)
+       -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
+       install-strip
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+       all all-am check check-am clean clean-binPROGRAMS \
+       clean-generic ctags ctags-recursive distclean \
+       distclean-compile distclean-generic distclean-hdr \
+       distclean-tags distdir dvi dvi-am html html-am info info-am \
+       install install-am install-binPROGRAMS install-data \
+       install-data-am install-dvi install-dvi-am install-exec \
+       install-exec-am install-html install-html-am install-info \
+       install-info-am install-man install-pdf install-pdf-am \
+       install-ps install-ps-am install-strip installcheck \
+       installcheck-am installdirs installdirs-am maintainer-clean \
+       maintainer-clean-generic mostlyclean mostlyclean-compile \
+       mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
+       uninstall uninstall-am uninstall-binPROGRAMS
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT: