hhsuite - amd64
Documentation
./doc/changelog.Debian.gz
./doc/examples/query.seq
./doc/examples/query.hhr.gz
./doc/examples/query.hhm.gz
./doc/examples/query.a3m.gz
./doc/copyright
./doc/README.gz
./doc/changelog.gz
Binaries
hhsearch
compile units
unassigned
hhworker.C
hhsearch.C
Class
./hhsearch.C.002t.class
Gimple
./hhsearch.C.004t.gimple
GKD
./hhsearch.o.gkd
OBJ
obj: ./hhsearch.o
util.C
list.C
hhalignment.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhhit.C
hash.C
hhhalfalignment.C
hhfullalignment.C
hhhitlist.C
hhfunc.C
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers/cs/pseudocounts.h
../headers/cs/utils.h
./hhhit.h
../headers/cs/library_pseudocounts.h
../headers/cs/profile_column.h
../headers/cs/vector.h
../headers/cs/context_library.h
../headers/cs/profile-inl.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
hhworker.C
hhsearch.C
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
util.C
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
list.C
./list.h
hhalignment.C
hhutil.C
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/xmmintrin.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
hhdecl.C
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/streambuf
hhmatrices.C
./hhhmm.h
hhhmm.C
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/pmmintrin.h
../headers/cs/count_profile.h
hhhit.C
hash.C
hhhalfalignment.C
hhfullalignment.C
./hhfullalignment.h
hhhitlist.C
hhfunc.C
../headers//usr/include/c++/4.9/bits/basic_string.tcc
./hash.h
../headers/cs/context_library-inl.h
../headers/cs/context_profile-inl.h
../headers/cs/library_pseudocounts-inl.h
../headers/cs/emission.h
../headers/cs/assert_helpers.h
./hhhitlist.h
../headers/cs/context_profile.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers/cs/io.h
../headers/cs/matrix.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/valarray_array.h
../headers//usr/include/c++/4.9/valarray
../headers//usr/include/c++/4.9/bits/slice_array.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/valarray_before.h
../headers//usr/include/c++/4.9/bits/gslice.h
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/pthread.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/stdint.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/blast_hits.h
../headers/cs/alignment.h
../headers/cs/count_profile-inl.h
../headers/cs/profile.h
../headers/cs/sequence.h
../headers/cs/sequence-inl.h
../headers/cs/alignment-inl.h
../headers/cs/substitution_matrix.h
./hhalignment.h
./hhhalfalignment.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/mm_malloc.h
../headers//usr/include/ctype.h
../headers//usr/include/unistd.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers/cs/blosum_matrix.h
../headers/cs/substitution_matrix-inl.h
../headers/cs/vector.h
../headers/cs/matrix.h
../headers/cs/utils.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/char_traits.h
blosum_matrix.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/substitution_matrix.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
as.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/as.h
../headers//usr/include/c++/4.9/new
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
log.cc
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers/cs/log.h
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/time.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/new
unassigned
../headers/cs/exception.h
../headers/cs/application.h
../headers/cs/getopt_pp.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
application.cc
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/log.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
unassigned
../headers/cs/getopt_pp.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
getopt_pp.cc
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/ctype.h
../headers//usr/include/unistd.h
assert_helpers.cc
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
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../headers//usr/include/wctype.h
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../headers//usr/include/c++/4.9/new
aa.cc
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../headers//usr/include/wctype.h
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../headers//usr/include/c++/4.9/new
libraries
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/librt.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/usr/lib/x86_64-linux-gnu/libgomp.so.1
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/hhsearch.1.gz
hhconsensus
compile units
unassigned
util.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhalignment.C
hhhalfalignment.C
hhfunc.C
hhconsensus.C
Class
./hhconsensus.C.002t.class
Gimple
./hhconsensus.C.004t.gimple
GKD
./hhconsensus.o.gkd
OBJ
obj: ./hhconsensus.o
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers/cs/pseudocounts.h
../headers/cs/utils.h
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util.C
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hhutil.C
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hhdecl.C
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../headers//usr/include/c++/4.9/streambuf
hhmatrices.C
./hhhmm.h
hhhmm.C
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/pmmintrin.h
../headers/cs/count_profile.h
hhalignment.C
hhhalfalignment.C
hhfunc.C
../headers//usr/include/c++/4.9/bits/basic_string.tcc
hhconsensus.C
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unassigned
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blosum_matrix.cc
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log.cc
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../headers//usr/include/c++/4.9/new
aa.cc
../headers//usr/include/c++/4.9/iostream
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libraries
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/usr/lib/x86_64-linux-gnu/libgomp.so.1
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
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../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/hhconsensus.1.gz
hhfilter
compile units
unassigned
util.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhalignment.C
hhfunc.C
hhfilter.C
Class
./hhfilter.C.002t.class
Gimple
./hhfilter.C.004t.gimple
GKD
./hhfilter.o.gkd
OBJ
obj: ./hhfilter.o
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/pseudocounts.h
../headers/cs/utils.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
util.C
../headers//usr/include/stdlib.h
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hhutil.C
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../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/xmmintrin.h
hhdecl.C
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hhmatrices.C
./hhhmm.h
hhhmm.C
../headers//usr/include/string.h
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../headers/cs/count_profile.h
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hhalignment.C
hhfunc.C
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hhfilter.C
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unassigned
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unassigned
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log.cc
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unassigned
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../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/ctype.h
../headers//usr/include/unistd.h
assert_helpers.cc
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers//usr/include/c++/4.9/new
aa.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers//usr/include/c++/4.9/new
libraries
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/usr/lib/x86_64-linux-gnu/libgomp.so.1
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/hhfilter.1.gz
ffindex_unpack
compile units
ffindex_unpack.c
ffutil.c
ffindex.c
includes
ffindex_unpack.c
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./ffindex.h
ffutil.c
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
ffindex.c
../headers//usr/include/sys/stat.h
../headers//usr/include/bits/types.h
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/time.h
../headers//usr/include/bits/stat.h
../headers//usr/include/bits/dirent.h
../headers//usr/include/search.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./ffindex.h
../headers//usr/include/dirent.h
libraries
manual
../man/ffindex_unpack.1.gz
hhalign
compile units
unassigned
hhalignment.C
util.C
list.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhhit.C
hash.C
hhhalfalignment.C
hhfullalignment.C
hhhitlist.C
hhfunc.C
hhalign.C
Class
./hhalign.C.002t.class
Gimple
./hhalign.C.004t.gimple
GKD
./hhalign.o.gkd
OBJ
obj: ./hhalign.o
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers/cs/pseudocounts.h
../headers/cs/utils.h
./hhhit.h
../headers/cs/library_pseudocounts.h
../headers/cs/profile_column.h
../headers/cs/vector.h
hhalignment.C
../headers/cs/context_library.h
../headers/cs/profile-inl.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
util.C
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
./list.h
list.C
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
hhutil.C
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/xmmintrin.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
hhdecl.C
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/streambuf
hhmatrices.C
./hhhmm.h
hhhmm.C
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/pmmintrin.h
../headers/cs/count_profile.h
hhhit.C
hash.C
hhhalfalignment.C
hhfullalignment.C
./hhfullalignment.h
hhhitlist.C
hhfunc.C
../headers//usr/include/c++/4.9/bits/basic_string.tcc
hhalign.C
./hash.h
../headers/cs/context_library-inl.h
../headers/cs/context_profile-inl.h
../headers/cs/library_pseudocounts-inl.h
../headers/cs/emission.h
../headers/cs/assert_helpers.h
./hhhitlist.h
../headers/cs/context_profile.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers/cs/io.h
../headers/cs/matrix.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/valarray_array.h
../headers//usr/include/c++/4.9/valarray
../headers//usr/include/c++/4.9/bits/slice_array.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/valarray_before.h
../headers//usr/include/c++/4.9/bits/gslice.h
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/stdint.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/blast_hits.h
../headers/cs/alignment.h
../headers/cs/count_profile-inl.h
../headers/cs/profile.h
../headers/cs/sequence.h
../headers/cs/sequence-inl.h
../headers/cs/alignment-inl.h
../headers/cs/substitution_matrix.h
./hhalignment.h
./hhhalfalignment.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/mm_malloc.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers/cs/blosum_matrix.h
../headers/cs/substitution_matrix-inl.h
../headers/cs/vector.h
../headers/cs/matrix.h
../headers/cs/utils.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/char_traits.h
blosum_matrix.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/substitution_matrix.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
as.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/as.h
../headers//usr/include/c++/4.9/new
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
log.cc
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers/cs/log.h
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/time.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/new
unassigned
../headers/cs/exception.h
../headers/cs/application.h
../headers/cs/getopt_pp.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
application.cc
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/log.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
unassigned
../headers/cs/getopt_pp.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
getopt_pp.cc
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/ctype.h
../headers//usr/include/unistd.h
assert_helpers.cc
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers//usr/include/c++/4.9/new
aa.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers//usr/include/c++/4.9/new
libraries
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/usr/lib/x86_64-linux-gnu/libgomp.so.1
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/hhalign.1.gz
ffindex_apply
compile units
ffindex_apply.c
ffutil.c
ffindex.c
includes
ffindex_apply.c
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/sys/types.h
../headers//usr/include/bits/sigset.h
../headers//usr/include/bits/siginfo.h
../headers//usr/include/signal.h
../headers//usr/include/bits/sigaction.h
./ffindex.h
ffutil.c
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
ffindex.c
../headers//usr/include/sys/stat.h
../headers//usr/include/bits/types.h
../headers//usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/stddef.h
../headers//usr/include/time.h
../headers//usr/include/bits/stat.h
../headers//usr/include/bits/dirent.h
../headers//usr/include/search.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./ffindex.h
../headers//usr/include/dirent.h
libraries
manual
../man/ffindex_apply.1.gz
hhblits
compile units
unassigned
hhalignment.C
hhworker.C
hhblits.C
Class
./hhblits.C.002t.class
Gimple
./hhblits.C.004t.gimple
GKD
./hhblits.o.gkd
OBJ
obj: ./hhblits.o
hhprefilter.C
util.C
list.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhhit.C
hhhalfalignment.C
hhfullalignment.C
hhhitlist.C
hhfunc.C
hash.C
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers/cs/pseudocounts.h
../headers/cs/utils.h
./hhhit.h
../headers/cs/library_pseudocounts.h
../headers/cs/profile_column.h
../headers/cs/vector.h
hhalignment.C
../headers/cs/context_library.h
../headers/cs/profile-inl.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
hhworker.C
hhblits.C
hhprefilter.C
util.C
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
list.C
./list.h
hhutil.C
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/xmmintrin.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
hhdecl.C
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/streambuf
hhmatrices.C
./hhhmm.h
hhhmm.C
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/pmmintrin.h
../headers/cs/count_profile.h
hhhit.C
hhhalfalignment.C
hhfullalignment.C
./hhfullalignment.h
hhhitlist.C
hhfunc.C
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/sstream
hash.C
./hash.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers/cs/context_library-inl.h
../headers/cs/context_profile-inl.h
../headers/cs/library_pseudocounts-inl.h
../headers/cs/emission.h
../headers/cs/assert_helpers.h
./hhhitlist.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers/cs/context_profile.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers/cs/io.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers/cs/matrix.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/valarray_array.h
../headers//usr/include/c++/4.9/valarray
../headers//usr/include/c++/4.9/bits/slice_array.h
../headers//usr/include/c++/4.9/bits/valarray_before.h
../headers//usr/include/c++/4.9/bits/gslice.h
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/pthread.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/ffindex.h
../headers//usr/include/stdint.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/blast_hits.h
../headers/cs/alignment.h
../headers/cs/count_profile-inl.h
../headers/cs/profile.h
../headers/cs/sequence.h
../headers/cs/sequence-inl.h
../headers/cs/alignment-inl.h
../headers/cs/substitution_matrix.h
./hhalignment.h
./hhhalfalignment.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/mm_malloc.h
../headers//usr/include/ctype.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/omp.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers/cs/exception.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers/cs/blosum_matrix.h
../headers/cs/substitution_matrix-inl.h
../headers/cs/vector.h
../headers/cs/matrix.h
../headers/cs/utils.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/char_traits.h
blosum_matrix.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/aa.h
../headers/cs/log.h
../headers/cs/substitution_matrix.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
as.cc
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/include/wchar.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/stdint.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers/cs/globals.h
../headers/cs/as.h
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unassigned
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aa.cc
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libraries
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manual
hhmake
compile units
unassigned
util.C
hhutil.C
hhdecl.C
hhmatrices.C
hhhmm.C
hhalignment.C
hhfunc.C
hhmake.C
Class
./hhmake.C.002t.class
Gimple
./hhmake.C.004t.gimple
GKD
./hhmake.o.gkd
OBJ
obj: ./hhmake.o
unassigned
blosum_matrix.cc
as.cc
unassigned
log.cc
unassigned
application.cc
unassigned
getopt_pp.cc
assert_helpers.cc
aa.cc
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
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util.C
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hhutil.C
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hhdecl.C
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hhmatrices.C
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hhhmm.C
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hhalignment.C
hhfunc.C
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hhmake.C
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unassigned
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blosum_matrix.cc
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