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Updated PhyloToL Part 2 (markdown)

Katzlab 2024-08-09 17:46:01 -04:00
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PhyloToL-Part-2.md

@ -39,6 +39,8 @@ To run the CL, use a similar command structure as described for running PhyloToL
| --sister_rules | in sisters mode | Path to a file | Sisters rules file | none |
| --subsister_rules | in subsisters mode | Path to a file | Subsisters rules file | none |
| --clade_grabbing_rules | in clade mode | Path to a file | Clade-grabbing rules file | none |
| --clade_grabbing_exceptions | no | Path to a file | List of taxa to _not_ remove for any reason | none |