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The output directory now contains a json file that is compatible with auspice.us. Both time scaled phylogenies and ancestral inferences can now be visualized and explored using auspice. Available colorings are "Date", "Genotype", "Branch support", and "Excluded". The first two work exactly like standard nextstrain/auspice viz.
In addition, this PR moves many functions that do IO for command line wrappers into a separate file
CLI_io.py
.