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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.
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.
Similar(49)
A Global-local search was performed with 10 SHMM and 3 PSIBLAST iterations; all other parameters were left as defaults.
All other settings were left as defaults.
All other parameters were left as defaults.
Other settings were left as defaults.
The maximum intron length was set to 6000 bp and other parameters were left as defaults.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com