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Update and rename phylotol.py to eukphylo.py
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# Author: Auden Cote-L'Heureux
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# This script is what users should call when running any or all components of
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# PhyloToL 6 part 2. It briefly determines which parts of the pipeline should be
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# EukPhylo part 2. It briefly determines which parts of the pipeline should be
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# run (pre-Guidance, Guidance, tree building, contamination loop, and/or
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# concatenation) based on the --start and --end parameters, and then runs all
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# of these components. Each component is actually run by the run() function in
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