1 Iteration.o: multipleAlign/Iteration.cpp config.h \
2 multipleAlign/Iteration.h multipleAlign/../alignment/Alignment.h \
3 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
4 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
5 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
6 /usr/include/bits/wordsize.h \
7 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
8 /usr/include/features.h /usr/include/sys/cdefs.h \
9 /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
10 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
11 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
12 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
13 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
14 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
15 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
16 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
17 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
18 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
19 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
20 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
21 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
22 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
23 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
24 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
25 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
26 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
27 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
28 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
29 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
30 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
31 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
32 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
33 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
34 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
35 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
36 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
37 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
38 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
39 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
40 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
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42 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
43 /usr/include/bits/wchar.h /usr/include/xlocale.h \
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46 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
47 /usr/include/locale.h /usr/include/bits/locale.h \
48 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
49 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
50 /usr/include/ctype.h /usr/include/bits/types.h \
51 /usr/include/bits/typesizes.h /usr/include/endian.h \
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53 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
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55 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
56 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
57 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
58 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
59 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
60 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
61 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
62 /usr/include/bits/sched.h /usr/include/bits/time.h \
63 /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
64 /usr/include/unistd.h /usr/include/bits/posix_opt.h \
65 /usr/include/bits/environments.h /usr/include/bits/confname.h \
66 /usr/include/getopt.h \
67 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
68 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
69 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
70 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
71 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
72 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
73 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
74 multipleAlign/../alignment/Sequence.h \
75 multipleAlign/../alignment/../general/userparams.h \
76 multipleAlign/../alignment/../general/UserParameters.h \
77 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
78 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
79 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
80 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
81 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
82 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
83 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
84 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
85 /usr/include/wctype.h \
86 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
87 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
88 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
89 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
90 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
91 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
92 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
93 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
94 multipleAlign/../alignment/../general/utils.h \
95 multipleAlign/../alignment/../general/Utility.h \
96 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
97 /usr/include/stdlib.h /usr/include/bits/waitflags.h \
98 /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
99 /usr/include/sys/select.h /usr/include/bits/select.h \
100 /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
101 /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
102 /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
103 /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
104 /usr/include/bits/errno.h /usr/include/linux/errno.h \
105 /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
106 /usr/include/asm-generic/errno-base.h \
107 multipleAlign/../alignment/../general/clustalw.h \
108 multipleAlign/../alignment/../general/general.h \
109 multipleAlign/../alignment/../general/Array2D.h \
110 multipleAlign/../alignment/../general/SquareMat.h \
111 multipleAlign/../alignment/../general/SymMatrix.h \
112 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
113 /usr/include/math.h /usr/include/bits/huge_val.h \
114 /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
115 /usr/include/bits/inf.h /usr/include/bits/nan.h \
116 /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
117 /usr/include/bits/mathinline.h \
118 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
119 multipleAlign/../alignment/../general/utils.h \
120 multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \
121 multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \
122 multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \
123 multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \
124 multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
125 multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
126 multipleAlign/../alignment/../general/VectorOutOfRange.h \
127 multipleAlign/../alignment/../general/SequenceNotFoundException.h \
128 multipleAlign/../general/clustalw.h \
129 multipleAlign/../alignment/ObjectiveScore.h \
130 multipleAlign/../alignment/../general/clustalw.h \
131 multipleAlign/../general/utils.h multipleAlign/../general/userparams.h \
132 multipleAlign/../tree/TreeInterface.h \
133 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
134 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
135 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
136 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \
137 multipleAlign/../tree/AlignmentSteps.h \
138 multipleAlign/../tree/../alignment/Alignment.h \
139 multipleAlign/../tree/../general/clustalw.h \
140 multipleAlign/../clustalw_version.h multipleAlign/MSA.h \
141 multipleAlign/ProfileBase.h multipleAlign/../tree/AlignmentSteps.h \
142 multipleAlign/ProfileAlignAlgorithm.h
146 multipleAlign/Iteration.h:
148 multipleAlign/../alignment/Alignment.h:
150 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:
152 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
154 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
156 /usr/include/bits/wordsize.h:
158 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
160 /usr/include/features.h:
162 /usr/include/sys/cdefs.h:
164 /usr/include/gnu/stubs.h:
166 /usr/include/gnu/stubs-64.h:
168 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
170 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
172 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
174 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h:
176 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
178 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:
180 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:
182 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h:
184 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h:
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188 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h:
190 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h:
192 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h:
194 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:
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202 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:
204 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
206 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
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212 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
214 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list:
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274 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:
276 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:
278 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h:
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312 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h:
314 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h:
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318 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
320 multipleAlign/../alignment/Sequence.h:
322 multipleAlign/../alignment/../general/userparams.h:
324 multipleAlign/../alignment/../general/UserParameters.h:
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