README.md
setup.py
asymmetree/__init__.py
asymmetree.egg-info/PKG-INFO
asymmetree.egg-info/SOURCES.txt
asymmetree.egg-info/dependency_links.txt
asymmetree.egg-info/requires.txt
asymmetree.egg-info/top_level.txt
asymmetree/best_matches/Augmentation.py
asymmetree/best_matches/ExtBestHits.py
asymmetree/best_matches/LRTConstructor.py
asymmetree/best_matches/Quartets.py
asymmetree/best_matches/TreeReconstruction.py
asymmetree/best_matches/TrueBMG.py
asymmetree/best_matches/__init__.py
asymmetree/cograph/Cograph.py
asymmetree/cograph/CographEditor.py
asymmetree/cograph/LinearCographDetector.py
asymmetree/cograph/__init__.py
asymmetree/file_io/ProteinOrthoParser.py
asymmetree/file_io/ScenarioFileIO.py
asymmetree/file_io/SeqFileIO.py
asymmetree/file_io/SubstModelIO.py
asymmetree/file_io/__init__.py
asymmetree/genome/GenomeSimulation.py
asymmetree/genome/__init__.py
asymmetree/paraphylo/SpeciesTreeFromParalogs.py
asymmetree/paraphylo/SpeciesTreeFromProteinOrtho.py
asymmetree/paraphylo/__init__.py
asymmetree/seqevolve/Alignment.py
asymmetree/seqevolve/EmpiricalModels.py
asymmetree/seqevolve/Evolver.py
asymmetree/seqevolve/EvolvingSequence.py
asymmetree/seqevolve/HetModel.py
asymmetree/seqevolve/IndelModel.py
asymmetree/seqevolve/SubstModel.py
asymmetree/seqevolve/__init__.py
asymmetree/tools/BuildST.py
asymmetree/tools/DistanceCalculation.py
asymmetree/tools/DoublyLinkedList.py
asymmetree/tools/GraphTools.py
asymmetree/tools/PhyloTree.py
asymmetree/tools/Tree.py
asymmetree/tools/__init__.py
asymmetree/tools/hdtgraph/DynamicGraph.py
asymmetree/tools/hdtgraph/ETTree.py
asymmetree/tools/hdtgraph/__init__.py
asymmetree/treeevolve/EvolutionRates.py
asymmetree/treeevolve/GeneTree.py
asymmetree/treeevolve/NoisyMatrix.py
asymmetree/treeevolve/Scenario.py
asymmetree/treeevolve/SpeciesTree.py
asymmetree/treeevolve/__init__.py
asymmetree/visualize/GeneTreeVis.py
asymmetree/visualize/__init__.py