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

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

diff --git a/binaries/src/clustalw/src/.deps/ProfileStandard.Po b/binaries/src/clustalw/src/.deps/ProfileStandard.Po
index e8bed5e..c0db6ce 100644 (file)
--- a/binaries/src/clustalw/src/.deps/ProfileStandard.Po
+++ b/binaries/src/clustalw/src/.deps/ProfileStandard.Po
@@ -1,150 +1,131 @@
-ProfileStandard.o ProfileStandard.o: multipleAlign/ProfileStandard.cpp \
-  config.h multipleAlign/ProfileStandard.h \
-  multipleAlign/../alignment/Alignment.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/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/bits/stl_algobase.h \
-  /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/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/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/include/bits/stdio_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/endian.h \
-  /usr/include/bits/endian.h /usr/include/sys/types.h \
-  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
-  /usr/include/time.h /usr/include/sys/select.h \
-  /usr/include/bits/select.h /usr/include/bits/sigset.h \
-  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
-  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
-  /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/cstdio \
-  /usr/include/stdio.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/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/sched.h /usr/include/bits/sched.h \
-  /usr/include/signal.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/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/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/exception \
-  /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_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 \
-  /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/bits/char_traits.h \
-  /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/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/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/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/iomanip \
-  /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/ios \
-  /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/locale_classes.h \
-  /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/istream.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/ostream \
-  /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/functional \
-  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
-  multipleAlign/../alignment/Sequence.h \
-  multipleAlign/../alignment/../general/userparams.h \
-  multipleAlign/../alignment/../general/UserParameters.h \
-  /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
-  multipleAlign/../alignment/../general/utils.h \
-  multipleAlign/../alignment/../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 \
-  multipleAlign/../alignment/../general/clustalw.h \
-  multipleAlign/../alignment/../general/general.h \
-  multipleAlign/../alignment/../general/Array2D.h \
-  multipleAlign/../alignment/../general/SquareMat.h \
-  multipleAlign/../alignment/../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 \
-  multipleAlign/../alignment/../general/utils.h \
-  multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \
-  multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \
-  multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \
-  multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \
-  multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
-  multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
-  multipleAlign/../alignment/../general/VectorOutOfRange.h \
-  multipleAlign/../alignment/../general/SequenceNotFoundException.h \
-  multipleAlign/ProfileBase.h
+ProfileStandard.o: multipleAlign/ProfileStandard.cpp config.h \
+ multipleAlign/ProfileStandard.h multipleAlign/../alignment/Alignment.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_algobase.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/4.4.7/../../../../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/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.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/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/exception \
+ /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/initializer_list \
+ /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/4.4.7/../../../../include/c++/4.4.7/string \
+ /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/char_traits.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/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/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/iosfwd \
+ /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/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/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/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /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/bits/locale_classes.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/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ multipleAlign/../alignment/Sequence.h \
+ multipleAlign/../alignment/../general/userparams.h \
+ multipleAlign/../alignment/../general/UserParameters.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/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/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 \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../general/Utility.h \
+ /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 /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/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 \
+ multipleAlign/../alignment/../general/clustalw.h \
+ multipleAlign/../alignment/../general/general.h \
+ multipleAlign/../alignment/../general/Array2D.h \
+ multipleAlign/../alignment/../general/SquareMat.h \
+ multipleAlign/../alignment/../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 \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
+ multipleAlign/../alignment/../general/VectorOutOfRange.h \
+ multipleAlign/../alignment/../general/SequenceNotFoundException.h \
+ multipleAlign/ProfileBase.h
 
 config.h:
 
@@ -152,19 +133,15 @@ multipleAlign/ProfileStandard.h:
 
 multipleAlign/../alignment/Alignment.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/functexcept.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/4.1.2/../../../../include/c++/4.1.2/exception_defines.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h:
-
-/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:
 
@@ -174,123 +151,131 @@ multipleAlign/../alignment/Alignment.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/cstring:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
 
-/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/stddef.h:
 
-/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/bits/functexcept.h:
 
-/usr/include/string.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
 
-/usr/include/xlocale.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/4.1.2/../../../../include/c++/4.1.2/climits:
+/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/4.1.2/include/limits.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/4.1.2/include/syslimits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h:
 
-/usr/include/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h:
 
-/usr/include/bits/posix1_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h:
 
-/usr/include/bits/local_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h:
 
-/usr/include/linux/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h:
 
-/usr/include/bits/posix2_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:
 
-/usr/include/bits/xopen_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h:
 
-/usr/include/bits/stdio_lim.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/c++/4.1.2/cstdlib:
+/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/stdlib.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:
 
-/usr/include/bits/waitflags.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
 
-/usr/include/bits/waitstatus.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
 
-/usr/include/endian.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:
 
-/usr/include/bits/endian.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h:
 
-/usr/include/sys/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
 
-/usr/include/bits/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list:
 
-/usr/include/bits/typesizes.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h:
 
-/usr/include/time.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:
 
-/usr/include/sys/select.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
 
-/usr/include/bits/select.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h:
 
-/usr/include/bits/sigset.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:
 
-/usr/include/bits/time.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h:
 
-/usr/include/sys/sysmacros.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar:
 
-/usr/include/bits/pthreadtypes.h:
+/usr/include/wchar.h:
 
-/usr/include/alloca.h:
+/usr/include/stdio.h:
 
-/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/stdarg.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h:
+/usr/include/bits/wchar.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio:
+/usr/include/xlocale.h:
 
-/usr/include/stdio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:
 
-/usr/include/libio.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/_G_config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale:
 
-/usr/include/wchar.h:
+/usr/include/locale.h:
 
-/usr/include/bits/wchar.h:
+/usr/include/bits/locale.h:
 
-/usr/include/gconv.h:
+/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/stdarg.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype:
 
-/usr/include/bits/sys_errlist.h:
+/usr/include/ctype.h:
 
-/usr/include/bits/stdio.h:
+/usr/include/bits/types.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale:
+/usr/include/bits/typesizes.h:
 
-/usr/include/locale.h:
+/usr/include/endian.h:
 
-/usr/include/bits/locale.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/ostream_insert.h:
 
-/usr/include/langinfo.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h:
 
-/usr/include/nl_types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h:
 
-/usr/include/iconv.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h:
 
-/usr/include/libintl.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/4.1.2/../../../../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/ext/atomicity.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/4.4.7/../../../../include/c++/4.4.7/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/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/signal.h:
+/usr/include/bits/time.h:
+
+/usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
 
@@ -304,147 +289,95 @@ multipleAlign/../alignment/Alignment.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/4.4.7/../../../../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/cwchar:
+/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/ctime:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip:
 
-/usr/include/stdint.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/4.1.2/../../../../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/locale_classes.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/4.4.7/../../../../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/stdexcept:
 
-/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/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/exception:
-
-/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_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:
-
-/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/bits/char_traits.h:
-
-/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/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/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/algorithm:
+multipleAlign/../alignment/Sequence.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h:
+multipleAlign/../alignment/../general/userparams.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h:
+multipleAlign/../alignment/../general/UserParameters.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/4.4.7/../../../../include/c++/4.4.7/iostream:
 
-/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/4.4.7/../../../../include/c++/4.4.7/ostream:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip:
+/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/istream:
+/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/ios:
+/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/localefwd.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/ios_base.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/bits/locale_classes.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/streambuf:
+/usr/include/wctype.h:
 
-/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/4.4.7/../../../../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/basic_ios.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/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/4.1.2/../../../../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/locale_facets.tcc:
 
-/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/bits/basic_ios.tcc:
 
-/usr/include/wctype.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/x86_64-redhat-linux/bits/ctype_base.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/ctype_inline.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/bits/codecvt.h:
+multipleAlign/../alignment/../general/utils.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:
+multipleAlign/../alignment/../general/Utility.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/4.4.7/../../../../include/c++/4.4.7/cstdlib:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc:
+/usr/include/stdlib.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc:
+/usr/include/bits/waitflags.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:
+/usr/include/bits/waitstatus.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:
+/usr/include/sys/types.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:
+/usr/include/sys/select.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream:
+/usr/include/bits/select.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc:
+/usr/include/bits/sigset.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:
+/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:
 
-multipleAlign/../alignment/Sequence.h:
+/usr/include/libio.h:
 
-multipleAlign/../alignment/../general/userparams.h:
+/usr/include/_G_config.h:
 
-multipleAlign/../alignment/../general/UserParameters.h:
+/usr/include/bits/stdio_lim.h:
 
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:
+/usr/include/bits/sys_errlist.h:
 
-multipleAlign/../alignment/../general/utils.h:
+/usr/include/bits/stdio.h:
 
-multipleAlign/../alignment/../general/Utility.h:
+/usr/include/string.h:
 
 /usr/include/errno.h:
 
@@ -454,8 +387,6 @@ multipleAlign/../alignment/../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:
@@ -470,7 +401,7 @@ multipleAlign/../alignment/../general/SquareMat.h:
 
 multipleAlign/../alignment/../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:
 
@@ -490,7 +421,7 @@ multipleAlign/../alignment/../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:
 
 multipleAlign/../alignment/../general/utils.h: