Clustal.o Clustal.o: Clustal.cpp config.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \
  /usr/include/bits/wordsize.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \
  /usr/include/string.h /usr/include/xlocale.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \
  /usr/include/stdio.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \
  /usr/include/gconv.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \
  /usr/include/locale.h /usr/include/bits/locale.h \
  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
  /usr/include/libintl.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \
  /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \
  /usr/include/bits/time.h /usr/include/signal.h \
  /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
  /usr/include/bits/setjmp.h /usr/include/unistd.h \
  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
  /usr/include/bits/confname.h /usr/include/getopt.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \
  /usr/include/ctype.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \
  /usr/include/stdint.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \
  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
  /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
  /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/sys/sysmacros.h /usr/include/alloca.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \
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  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
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  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
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  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
  /usr/include/wctype.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \
  Clustal.h general/clustalw.h general/general.h general/Array2D.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
  general/SquareMat.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
  general/SymMatrix.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
  /usr/include/math.h /usr/include/bits/huge_val.h \
  /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/bits/mathinline.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
  general/utils.h general/Utility.h /usr/include/errno.h \
  /usr/include/bits/errno.h /usr/include/linux/errno.h \
  /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
  /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
  general/clustalw.h general/userparams.h general/UserParameters.h \
  general/utils.h fileInput/FileReader.h \
  fileInput/../alignment/Alignment.h fileInput/../alignment/Sequence.h \
  fileInput/../alignment/../general/userparams.h \
  fileInput/../alignment/../general/utils.h \
  fileInput/../alignment/../substitutionMatrix/globalmatrix.h \
  fileInput/../alignment/../substitutionMatrix/SubMatrix.h \
  fileInput/../alignment/../substitutionMatrix/../general/clustalw.h \
  fileInput/../alignment/../substitutionMatrix/../general/userparams.h \
  fileInput/../alignment/../substitutionMatrix/../general/utils.h \
  fileInput/../alignment/../substitutionMatrix/../general/Array2D.h \
  fileInput/../alignment/../general/VectorOutOfRange.h \
  fileInput/../alignment/../general/SequenceNotFoundException.h \
  fileInput/../alignment/Sequence.h fileInput/../general/userparams.h \
  fileInput/../general/utils.h fileInput/FileParser.h \
  fileInput/InFileStream.h fileInput/ClustalFileParser.h \
  fileInput/PearsonFileParser.h fileInput/PIRFileParser.h \
  fileInput/GDEFileParser.h fileInput/MSFFileParser.h \
  fileInput/RSFFileParser.h fileInput/EMBLFileParser.h \
  alignment/Alignment.h alignment/AlignmentOutput.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \
  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert \
  /usr/include/assert.h alignment/Alignment.h \
  pairwise/FullPairwiseAlign.h pairwise/PairwiseAlignBase.h \
  pairwise/../alignment/Alignment.h pairwise/FastPairwiseAlign.h \
  multipleAlign/MSA.h multipleAlign/ProfileBase.h \
  multipleAlign/../alignment/Alignment.h \
  multipleAlign/../tree/AlignmentSteps.h \
  multipleAlign/ProfileAlignAlgorithm.h \
  multipleAlign/LowScoreSegProfile.h multipleAlign/Iteration.h \
  multipleAlign/../general/clustalw.h tree/TreeInterface.h \
  tree/AlignmentSteps.h tree/../alignment/Alignment.h \
  tree/../general/clustalw.h general/debuglogObject.h general/DebugLog.h \
  general/statsObject.h general/Stats.h alignment/ObjectiveScore.h \
  alignment/../general/clustalw.h \
  alignment/../substitutionMatrix/globalmatrix.h \
  general/ClustalWResources.h Help.h

config.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:

/usr/include/bits/wordsize.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:

/usr/include/features.h:

/usr/include/sys/cdefs.h:

/usr/include/gnu/stubs.h:

/usr/include/gnu/stubs-64.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:

/usr/include/string.h:

/usr/include/xlocale.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio:

/usr/include/stdio.h:

/usr/include/bits/types.h:

/usr/include/bits/typesizes.h:

/usr/include/libio.h:

/usr/include/_G_config.h:

/usr/include/wchar.h:

/usr/include/bits/wchar.h:

/usr/include/gconv.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h:

/usr/include/bits/stdio_lim.h:

/usr/include/bits/sys_errlist.h:

/usr/include/bits/stdio.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale:

/usr/include/locale.h:

/usr/include/bits/locale.h:

/usr/include/langinfo.h:

/usr/include/nl_types.h:

/usr/include/iconv.h:

/usr/include/libintl.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h:

/usr/include/pthread.h:

/usr/include/endian.h:

/usr/include/bits/endian.h:

/usr/include/sched.h:

/usr/include/time.h:

/usr/include/bits/sched.h:

/usr/include/bits/time.h:

/usr/include/signal.h:

/usr/include/bits/sigset.h:

/usr/include/bits/pthreadtypes.h:

/usr/include/bits/setjmp.h:

/usr/include/unistd.h:

/usr/include/bits/posix_opt.h:

/usr/include/bits/environments.h:

/usr/include/bits/confname.h:

/usr/include/getopt.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype:

/usr/include/ctype.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime:

/usr/include/stdint.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h:

/usr/include/limits.h:

/usr/include/bits/posix1_lim.h:

/usr/include/bits/local_lim.h:

/usr/include/linux/limits.h:

/usr/include/bits/posix2_lim.h:

/usr/include/bits/xopen_lim.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib:

/usr/include/stdlib.h:

/usr/include/bits/waitflags.h:

/usr/include/bits/waitstatus.h:

/usr/include/sys/types.h:

/usr/include/sys/select.h:

/usr/include/bits/select.h:

/usr/include/sys/sysmacros.h:

/usr/include/alloca.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype:

/usr/include/wctype.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc:

Clustal.h:

general/clustalw.h:

general/general.h:

general/Array2D.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc:

general/SquareMat.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:

general/SymMatrix.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath:

/usr/include/math.h:

/usr/include/bits/huge_val.h:

/usr/include/bits/huge_valf.h:

/usr/include/bits/huge_vall.h:

/usr/include/bits/inf.h:

/usr/include/bits/nan.h:

/usr/include/bits/mathdef.h:

/usr/include/bits/mathcalls.h:

/usr/include/bits/mathinline.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:

general/utils.h:

general/Utility.h:

/usr/include/errno.h:

/usr/include/bits/errno.h:

/usr/include/linux/errno.h:

/usr/include/asm/errno.h:

/usr/include/asm-x86_64/errno.h:

/usr/include/asm-generic/errno.h:

/usr/include/asm-generic/errno-base.h:

general/clustalw.h:

general/userparams.h:

general/UserParameters.h:

general/utils.h:

fileInput/FileReader.h:

fileInput/../alignment/Alignment.h:

fileInput/../alignment/Sequence.h:

fileInput/../alignment/../general/userparams.h:

fileInput/../alignment/../general/utils.h:

fileInput/../alignment/../substitutionMatrix/globalmatrix.h:

fileInput/../alignment/../substitutionMatrix/SubMatrix.h:

fileInput/../alignment/../substitutionMatrix/../general/clustalw.h:

fileInput/../alignment/../substitutionMatrix/../general/userparams.h:

fileInput/../alignment/../substitutionMatrix/../general/utils.h:

fileInput/../alignment/../substitutionMatrix/../general/Array2D.h:

fileInput/../alignment/../general/VectorOutOfRange.h:

fileInput/../alignment/../general/SequenceNotFoundException.h:

fileInput/../alignment/Sequence.h:

fileInput/../general/userparams.h:

fileInput/../general/utils.h:

fileInput/FileParser.h:

fileInput/InFileStream.h:

fileInput/ClustalFileParser.h:

fileInput/PearsonFileParser.h:

fileInput/PIRFileParser.h:

fileInput/GDEFileParser.h:

fileInput/MSFFileParser.h:

fileInput/RSFFileParser.h:

fileInput/EMBLFileParser.h:

alignment/Alignment.h:

alignment/AlignmentOutput.h:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert:

/usr/include/assert.h:

alignment/Alignment.h:

pairwise/FullPairwiseAlign.h:

pairwise/PairwiseAlignBase.h:

pairwise/../alignment/Alignment.h:

pairwise/FastPairwiseAlign.h:

multipleAlign/MSA.h:

multipleAlign/ProfileBase.h:

multipleAlign/../alignment/Alignment.h:

multipleAlign/../tree/AlignmentSteps.h:

multipleAlign/ProfileAlignAlgorithm.h:

multipleAlign/LowScoreSegProfile.h:

multipleAlign/Iteration.h:

multipleAlign/../general/clustalw.h:

tree/TreeInterface.h:

tree/AlignmentSteps.h:

tree/../alignment/Alignment.h:

tree/../general/clustalw.h:

general/debuglogObject.h:

general/DebugLog.h:

general/statsObject.h:

general/Stats.h:

alignment/ObjectiveScore.h:

alignment/../general/clustalw.h:

alignment/../substitutionMatrix/globalmatrix.h:

general/ClustalWResources.h:

Help.h: