multiple-hits option with BUSTED-PH

[Emilyaoc]

Hello,

Please could I just check that I understand correctly that BUSTED-PH does not currently include the option to account for multiple nucleotide substitutions as is available in the standard version of BUSTED (--multiple-hits)?

Thank you

Emily

[agselberg]

Hi Emily,

Right now our BUSTED-PH does not have the option to account for multiple nucleotide substitutions. However if you would prefer to use multi-hit in your BUSTED-PH analyses you could do that (in a somewhat clunky way) by running regular busted three times on the same data but with different test branches. For example (using test data positive-test.fas)

1. Run BUSTED+MH on Foreground branches
   hyphy busted --alignment examples/positive-test.fas --output FG-BUSTED.json --branches Primates --multiple-hits Double+Triple

2. Run BUSTED+MH on background branches
   hyphy busted --alignment examples/positive-test.fas --output BG-BUSTED.json --branches 'Unlabeled branches' --multiple-hits Double+Triple

3. Run BUSTED+MH on all branches
   hyphy busted --alignment examples/positive-test.fas --output ALL-BUSTED.json --multiple-hits Double+Triple

4. Wrap the results together and get p-values using wrapper.bf.zip
   hyphy wrapper.bf FG-BUSTED.json BG-BUSTED.json ALL-BUSTED.json BUSTED-PH.json

Best,
Avery