README.md
setup.py
ragout/__init__.py
ragout/__version__.py
ragout/main.py
ragout/six.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/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/chimera_detector.py
ragout/breakpoint_graph/inferer.py
ragout/breakpoint_graph/permutation.py
ragout/breakpoint_graph/repeat_resolver.py
ragout/maf2synteny/__init__.py
ragout/maf2synteny/maf2synteny.py
ragout/newick/__init__.py
ragout/newick/lexer.py
ragout/newick/parser.py
ragout/newick/tokens.py
ragout/newick/tree.py
ragout/overlap/__init__.py
ragout/overlap/overlap.py
ragout/parsers/__init__.py
ragout/parsers/fasta_parser.py
ragout/parsers/phylogeny_parser.py
ragout/parsers/recipe_parser.py
ragout/phylogeny/__init__.py
ragout/phylogeny/inferer.py
ragout/phylogeny/phylogeny.py
ragout/scaffolder/__init__.py
ragout/scaffolder/merge_iters.py
ragout/scaffolder/output_generator.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/hal.py
ragout/synteny_backend/maf.py
ragout/synteny_backend/sibelia.py
ragout/synteny_backend/synteny_backend.py
ragout/tests/__init__.py
ragout/tests/test_toy.py
ragout/tests/data/DH1.fasta
ragout/tests/data/ecoli.rcp
ragout/tests/data/mg1655.coords
ragout/tests/data/mg1655_contigs.fasta