JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

[jabaws.git] / binaries / src / clustalw / src / .deps / Clustal.Po

diff --git a/binaries/src/clustalw/src/.deps/Clustal.Po b/binaries/src/clustalw/src/.deps/Clustal.Po
index 0392e41..df48e20 100644 (file)
--- a/binaries/src/clustalw/src/.deps/Clustal.Po
+++ b/binaries/src/clustalw/src/.deps/Clustal.Po
@@ -1,184 +1,171 @@
-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 \
-  /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
+Clustal.o: Clustal.cpp config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ Clustal.h general/clustalw.h general/general.h general/Array2D.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h general/utils.h general/Utility.h \
+ /usr/include/string.h /usr/include/errno.h /usr/include/bits/errno.h \
+ /usr/include/linux/errno.h /usr/include/asm/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 \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.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/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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 \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime
 
 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/4.4.7/../../../../include/c++/4.4.7/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/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -188,78 +175,98 @@ config.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/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/ostream:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
 
-/usr/include/string.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
 
 /usr/include/xlocale.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
 
-/usr/include/stdio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:
 
-/usr/include/bits/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
 
-/usr/include/bits/typesizes.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h:
 
-/usr/include/libio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
 
-/usr/include/_G_config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:
 
-/usr/include/wchar.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:
 
-/usr/include/bits/wchar.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h:
 
-/usr/include/gconv.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h:
 
-/usr/include/bits/stdio_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h:
 
-/usr/include/bits/sys_errlist.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h:
 
-/usr/include/bits/stdio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:
 
-/usr/include/locale.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h:
 
-/usr/include/bits/locale.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:
 
-/usr/include/langinfo.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h:
 
-/usr/include/nl_types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale:
 
-/usr/include/iconv.h:
+/usr/include/locale.h:
 
-/usr/include/libintl.h:
+/usr/include/bits/locale.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/4.4.7/../../../../include/c++/4.4.7/cctype:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h:
+/usr/include/ctype.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/bits/types.h:
 
-/usr/include/pthread.h:
+/usr/include/bits/typesizes.h:
 
 /usr/include/endian.h:
 
 /usr/include/bits/endian.h:
 
+/usr/include/bits/byteswap.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
 /usr/include/sched.h:
 
 /usr/include/time.h:
@@ -268,10 +275,6 @@ config.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:
@@ -286,167 +289,85 @@ config.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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.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/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h:
 
-/usr/include/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:
 
-/usr/include/bits/posix1_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
 
-/usr/include/bits/local_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h:
 
-/usr/include/linux/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h:
 
-/usr/include/bits/posix2_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h:
 
-/usr/include/bits/xopen_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:
 
-/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/4.4.7/../../../../include/c++/4.4.7/initializer_list:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/streambuf:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.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/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.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/4.4.7/../../../../include/c++/4.4.7/cwctype:
 
-/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/include/wctype.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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.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/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h:
 
-/usr/include/wctype.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/istream:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc:
 
-/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/4.4.7/../../../../include/c++/4.4.7/fstream:
 
-/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/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h:
 
-/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/4.4.7/../../../../include/c++/4.4.7/cstdio:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:
+/usr/include/libio.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:
+/usr/include/_G_config.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:
+/usr/include/bits/stdio_lim.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream:
+/usr/include/bits/sys_errlist.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc:
+/usr/include/bits/stdio.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h:
 
-/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/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc:
 
 Clustal.h:
 
@@ -456,23 +377,25 @@ 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/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.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/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
 
-general/SquareMat.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip:
+general/SquareMat.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip:
 
 general/SymMatrix.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:
 
 /usr/include/math.h:
 
@@ -492,14 +415,36 @@ general/SymMatrix.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/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/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/bits/sigset.h:
+
+/usr/include/sys/sysmacros.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/include/alloca.h:
 
 general/utils.h:
 
 general/Utility.h:
 
+/usr/include/string.h:
+
 /usr/include/errno.h:
 
 /usr/include/bits/errno.h:
@@ -508,8 +453,6 @@ general/Utility.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:
@@ -524,6 +467,14 @@ general/utils.h:
 
 fileInput/FileReader.h:
 
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h:
+
 fileInput/../alignment/Alignment.h:
 
 fileInput/../alignment/Sequence.h:
@@ -576,11 +527,11 @@ 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/4.4.7/../../../../include/c++/4.4.7/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/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert:
 
 /usr/include/assert.h:
 
@@ -635,3 +586,5 @@ alignment/../substitutionMatrix/globalmatrix.h:
 general/ClustalWResources.h:
 
 Help.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime: