README.md
muller.py
setup.py
muller/__init__.py
muller/__main__.py
muller/commandline_parser.py
muller/muller_workflow.py
muller/treetools.py
muller/widgets.py
muller.egg-info/PKG-INFO
muller.egg-info/SOURCES.txt
muller.egg-info/dependency_links.txt
muller.egg-info/requires.txt
muller.egg-info/top_level.txt
muller/clustering/__init__.py
muller/clustering/filters.py
muller/clustering/generate_genotypes.py
muller/clustering/mutational_distances.py
muller/clustering/methods/__init__.py
muller/clustering/methods/difference.py
muller/clustering/methods/hierarchical_method.py
muller/clustering/methods/population_genotypes_cache.py
muller/clustering/methods/twostep_method.py
muller/clustering/metrics/__init__.py
muller/clustering/metrics/calculation.py
muller/clustering/metrics/distance.py
muller/clustering/metrics/pairwise_calculation_cache.py
muller/dataio/__init__.py
muller/dataio/file_parsers.py
muller/dataio/tables.py
muller/dataio/trajectories.py
muller/graphics/__init__.py
muller/graphics/dendrogram.py
muller/graphics/flowchart.py
muller/graphics/generate_muller_plot.py
muller/graphics/genotype_plots.py
muller/graphics/heatmap.py
muller/inheritance/__init__.py
muller/inheritance/cluster.py
muller/inheritance/order.py
muller/inheritance/order_by_area.py
muller/inheritance/scoring.py
muller/inheritance/sort_genotypes.py
muller/inheritance/timepoint_detection.py
muller/muller_output/__init__.py
muller/muller_output/generate_scripts.py
muller/muller_output/generate_tables.py
muller/muller_output/save_output.py
muller/palettes/__init__.py
muller/palettes/colorset.py
muller/palettes/general.py
muller/palettes/palette_annotation.py
muller/palettes/palette_distinctive.py
muller/palettes/palette_lineage.py