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All remaining settings can be left as default, or feel free to modify as per your preferences.
The rest of the Magic Button options should be left as default (Close Active Window, 400, Show Clock and 2 Icons).
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The other fields are left as default.
For docking, the extra precision (XP) mode was used both for the actives and decoy sets and all settings were left as default except for adding the Epik states penalties to the docking score.
For all forward and reverse BLASTp searches, E value cut-off was set to 1E-20 (-e 1E-20), output was set to tabular (-m 8), all other parameters were left as default.
All other parameters were left as default values.
The guide tree was estimated by the program, and all other parameters were left as default.
All other settings were left as default, with 1000 replicates for bootstrapping.
The refractive index of the 10 mM pH 5 acetate buffer was found to be close to water, and thus, the η value used was left as default.
Nearly all of the priors were left as default, except for the relative rate parameters for the codon positions, which were set to a finite uniform prior.
Parameter settings are described in the Supplementary Note and in general have been left as default or set to recommended values based on the literature.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com