Phylo - Phylogenesis library

.directory

@@ -0,0 +1,4 @@
+[Dolphin]
+Timestamp=2015,7,11,17,31,9
+Version=3
+VisibleRoles=Icons_text

.gitignore

@@ -40,4 +40,10 @@ Lobo/Tests/*.a
 Lobo/Tests/*.o
 tools/*.o
 tools/*.a
-tools/Depend
+tools/Depend
+Phylo/Sources/*.o
+Phylo/Sources/*.a
+Phylo/APPS/*.o
+Phylo/APPS/*.a
+Phylo/Tests/*.o
+Phylo/Test/*.a

Align2/APPS/Depend

@@ -0,0 +1,168 @@
+subali.o: subali.cc /usr/include/stdc-predef.h \
+ ../../Align2/Sources/ScoringS2S.h ../../Align2/Sources/ScoringScheme.h \
+ ../../Align2/Sources/AlignmentData.h ../../Align2/Sources/Alignment.h \
+ ../../Align2/Sources/AlignmentBase.h ../../tools/Debug.h \
+ /usr/include/c++/4.9/exception \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \
+ /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \
+ /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \
+ /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/sigset.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/select2.h \
+ /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/x86_64-linux-gnu/bits/stdlib.h \
+ /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \
+ /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \
+ /usr/include/c++/4.9/bits/stringfwd.h \
+ /usr/include/c++/4.9/bits/memoryfwd.h \
+ /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar2.h \
+ /usr/include/c++/4.9/bits/char_traits.h \
+ /usr/include/c++/4.9/bits/stl_algobase.h \
+ /usr/include/c++/4.9/bits/functexcept.h \
+ /usr/include/c++/4.9/bits/exception_defines.h \
+ /usr/include/c++/4.9/bits/cpp_type_traits.h \
+ /usr/include/c++/4.9/ext/type_traits.h \
+ /usr/include/c++/4.9/ext/numeric_traits.h \
+ /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \
+ /usr/include/c++/4.9/bits/concept_check.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.9/debug/debug.h \
+ /usr/include/c++/4.9/bits/stl_iterator.h \
+ /usr/include/c++/4.9/bits/ptr_traits.h \
+ /usr/include/c++/4.9/bits/predefined_ops.h \
+ /usr/include/c++/4.9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \
+ /usr/include/c++/4.9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \
+ /usr/include/c++/4.9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \
+ /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \
+ /usr/include/c++/4.9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \
+ /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \
+ /usr/include/c++/4.9/bits/ostream_insert.h \
+ /usr/include/c++/4.9/bits/cxxabi_forced.h \
+ /usr/include/c++/4.9/bits/stl_function.h \
+ /usr/include/c++/4.9/backward/binders.h \
+ /usr/include/c++/4.9/bits/range_access.h \
+ /usr/include/c++/4.9/bits/basic_string.h \
+ /usr/include/c++/4.9/bits/basic_string.tcc \
+ /usr/include/c++/4.9/bits/locale_classes.tcc \
+ /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.h \
+ /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \
+ /usr/include/c++/4.9/bits/streambuf_iterator.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \
+ /usr/include/c++/4.9/bits/locale_facets.tcc \
+ /usr/include/c++/4.9/bits/basic_ios.tcc \
+ /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \
+ /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \
+ /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio2.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \
+ /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \
+ /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \
+ /usr/include/c++/4.9/bits/stl_construct.h \
+ /usr/include/c++/4.9/ext/alloc_traits.h \
+ /usr/include/c++/4.9/bits/stl_uninitialized.h \
+ /usr/include/c++/4.9/bits/stl_vector.h \
+ /usr/include/c++/4.9/bits/stl_bvector.h \
+ /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \
+ /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \
+ ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \
+ ../../tools/std.h /usr/include/math.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_val.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
+ /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
+ /usr/include/x86_64-linux-gnu/bits/inf.h \
+ /usr/include/x86_64-linux-gnu/bits/nan.h \
+ /usr/include/x86_64-linux-gnu/bits/mathdef.h \
+ /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
+ /usr/include/x86_64-linux-gnu/bits/mathinline.h \
+ /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/sstream \
+ /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \
+ /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \
+ /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \
+ /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \
+ /usr/include/c++/4.9/bits/algorithmfwd.h \
+ /usr/include/c++/4.9/bits/stl_heap.h \
+ /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Align2/Sources/Structure.h \
+ ../../Align2/Sources/SubMatrix.h ../../Align2/Sources/Substitution.h \
+ ../../Align2/Sources/ScoringP2S.h ../../Align2/Sources/Profile.h \
+ ../../Biopool/Sources/AminoAcidCode.h ../../Align2/Sources/ScoringP2P.h \
+ ../../Align2/Sources/ScoringFunction.h \
+ ../../Align2/Sources/HenikoffProfile.h \
+ ../../Align2/Sources/PSICProfile.h \
+ ../../Align2/Sources/SeqDivergenceProfile.h \
+ ../../Align2/Sources/AGPFunction.h ../../Align2/Sources/GapFunction.h \
+ ../../Align2/Sources/NWAlign.h ../../Align2/Sources/Align.h \
+ ../../Align2/Sources/Traceback.h ../../Align2/Sources/SequenceData.h \
+ ../../Align2/Sources/CrossProduct.h ../../Align2/Sources/LogAverage.h \
+ ../../Align2/Sources/DotPFreq.h ../../Align2/Sources/DotPOdds.h \
+ ../../Align2/Sources/EDistance.h ../../Align2/Sources/Pearson.h \
+ ../../Align2/Sources/JensenShannon.h \
+ ../../Align2/Sources/AtchleyDistance.h \
+ ../../Align2/Sources/AtchleyCorrelation.h ../../Align2/Sources/SWAlign.h \
+ ../../Align2/Sources/FSAlign.h ../../Align2/Sources/VGPFunction.h \
+ ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \
+ /usr/include/x86_64-linux-gnu/bits/string3.h \
+ ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \
+ ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \
+ ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \
+ ../../Biopool/Sources/Identity.h ../../Biopool/Sources/Monomer.h \
+ ../../Biopool/Sources/Component.h ../../Biopool/Sources/Bond.h \
+ ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \
+ ../../Biopool/Sources/SideChain.h \
+ ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Spacer.h \
+ ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \
+ /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \
+ /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \
+ /usr/include/c++/4.9/bits/stl_set.h \
+ /usr/include/c++/4.9/bits/stl_multiset.h \
+ ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \
+ ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \
+ ../../Biopool/Sources/SolvExpos.h ../../Align2/Sources/VGPFunction2.h \
+ ../../Align2/Sources/Sec.h ../../Align2/Sources/Ss2.h \
+ ../../Align2/Sources/Ss2Input.h ../../Align2/Sources/Prof.h \
+ ../../Align2/Sources/ProfInput.h ../../Align2/Sources/stringtools.h \
+ ../../Align2/Sources/SecSequenceData.h ../../tools/GetArg.h \
+ /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \
+ ../../tools/String2Number.h /usr/include/c++/4.9/ctime