README.md
setup.py
src/asymmetree/__init__.py
src/asymmetree.egg-info/PKG-INFO
src/asymmetree.egg-info/SOURCES.txt
src/asymmetree.egg-info/dependency_links.txt
src/asymmetree.egg-info/requires.txt
src/asymmetree.egg-info/top_level.txt
src/asymmetree/best_matches/Augmentation.py
src/asymmetree/best_matches/BMGEditing.py
src/asymmetree/best_matches/ExtBestHits.py
src/asymmetree/best_matches/LeastResolvedTree.py
src/asymmetree/best_matches/Quartets.py
src/asymmetree/best_matches/TreeReconstruction.py
src/asymmetree/best_matches/TrueBMG.py
src/asymmetree/best_matches/__init__.py
src/asymmetree/cograph/Cograph.py
src/asymmetree/cograph/CographEditor.py
src/asymmetree/cograph/__init__.py
src/asymmetree/cograph/testfile_ClusterDeletion.py
src/asymmetree/datastructures/AVLTree.py
src/asymmetree/datastructures/DoublyLinkedList.py
src/asymmetree/datastructures/LinkedList.py
src/asymmetree/datastructures/Partition.py
src/asymmetree/datastructures/PhyloTree.py
src/asymmetree/datastructures/Tree.py
src/asymmetree/datastructures/__init__.py
src/asymmetree/datastructures/hdtgraph/DynamicGraph.py
src/asymmetree/datastructures/hdtgraph/ETTree.py
src/asymmetree/datastructures/hdtgraph/__init__.py
src/asymmetree/file_io/ProteinOrthoParser.py
src/asymmetree/file_io/ScenarioFileIO.py
src/asymmetree/file_io/SeqFileIO.py
src/asymmetree/file_io/SubstModelIO.py
src/asymmetree/file_io/__init__.py
src/asymmetree/genome/GenomeSimulation.py
src/asymmetree/genome/__init__.py
src/asymmetree/hgt/Fitch.py
src/asymmetree/hgt/TimeComparison.py
src/asymmetree/hgt/__init__.py
src/asymmetree/paraphylo/SpeciesTreeFromParalogs.py
src/asymmetree/paraphylo/SpeciesTreeFromProteinOrtho.py
src/asymmetree/paraphylo/__init__.py
src/asymmetree/seqevolve/Alignment.py
src/asymmetree/seqevolve/EmpiricalModels.py
src/asymmetree/seqevolve/Evolver.py
src/asymmetree/seqevolve/EvolvingSequence.py
src/asymmetree/seqevolve/HetModel.py
src/asymmetree/seqevolve/IndelModel.py
src/asymmetree/seqevolve/SubstModel.py
src/asymmetree/seqevolve/__init__.py
src/asymmetree/tools/Build.py
src/asymmetree/tools/BuildST.py
src/asymmetree/tools/DistanceCalculation.py
src/asymmetree/tools/GraphTools.py
src/asymmetree/tools/Partitioning.py
src/asymmetree/tools/Sampling.py
src/asymmetree/tools/__init__.py
src/asymmetree/treeevolve/EvolutionRates.py
src/asymmetree/treeevolve/GeneTree.py
src/asymmetree/treeevolve/NoisyMatrix.py
src/asymmetree/treeevolve/Scenario.py
src/asymmetree/treeevolve/SpeciesTree.py
src/asymmetree/treeevolve/__init__.py
src/asymmetree/visualize/GeneTreeVis.py
src/asymmetree/visualize/__init__.py