MANIFEST.in
README.md
ez_setup.py
setup.py
docs/INSTALL.md
docs/USAGE.md
ragout/__init__.py
ragout/main.py
ragout.egg-info/PKG-INFO
ragout.egg-info/SOURCES.txt
ragout.egg-info/dependency_links.txt
ragout.egg-info/entry_points.txt
ragout.egg-info/requires.txt
ragout.egg-info/top_level.txt
ragout/assembly_graph/__init__.py
ragout/assembly_graph/assembly_refine.py
ragout/breakpoint_graph/__init__.py
ragout/breakpoint_graph/breakpoint_graph.py
ragout/breakpoint_graph/permutation.py
ragout/breakpoint_graph/phylogeny.py
ragout/maf2synteny/__init__.py
ragout/maf2synteny/maf2synteny.py
ragout/maf2synteny/cpp_impl/breakpoint_graph.cpp
ragout/maf2synteny/cpp_impl/breakpoint_graph.h
ragout/maf2synteny/cpp_impl/compress_algorithms.cpp
ragout/maf2synteny/cpp_impl/compress_algorithms.h
ragout/maf2synteny/cpp_impl/disjoint_set.h
ragout/maf2synteny/cpp_impl/maf_tools.cpp
ragout/maf2synteny/cpp_impl/maf_tools.h
ragout/maf2synteny/cpp_impl/main.cpp
ragout/maf2synteny/cpp_impl/permutation.cpp
ragout/maf2synteny/cpp_impl/permutation.h
ragout/maf2synteny/cpp_impl/utility.h
ragout/overlap/__init__.py
ragout/overlap/overlap.py
ragout/overlap/cpp_impl/fasta.cpp
ragout/overlap/cpp_impl/fasta.h
ragout/overlap/cpp_impl/main.cpp
ragout/overlap/cpp_impl/overlap.cpp
ragout/overlap/cpp_impl/overlap.h
ragout/parsers/__init__.py
ragout/parsers/config_parser.py
ragout/scaffolder/__init__.py
ragout/scaffolder/merge_iters.py
ragout/scaffolder/scaffolder.py
ragout/shared/__init__.py
ragout/shared/config.py
ragout/shared/datatypes.py
ragout/shared/debug.py
ragout/shared/utils.py
ragout/synteny_backend/__init__.py
ragout/synteny_backend/cactus.py
ragout/synteny_backend/sibelia.py
ragout/synteny_backend/synteny_backend.py
scripts/debug-report.py
scripts/dotplot.py
scripts/install-sibelia.py
scripts/ord2fasta.py
scripts/verify-order.py
scripts/utils/__init__.py
scripts/utils/nucmer_parser.py