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Update run_eukphylo.sh
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## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop).
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## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
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parent='/PhyloToL-6/PTL2'
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parent='/EukPhylo/PTL2'
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out_dir='/Output_data'
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in_dir='/Input_data'
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