Thanks. I'm still missing something, though.
I can now save, modify, and open the lf just fine. When I try opening CodonMutationToTreeMapper.bf, I get:
Quote:Likelihood Functionlf has not been initialized
Current BL Command:Reconstruct Ancestors into ancestralSeqs from the likelihood function lf Current Task has been terminated. Would you like to see the remaining error messages, if there are any?
Clicking 'yes':
Quote:Problem occurred in line:setupMapToTree(0)
Current BL Command:setupMapToTree(0) Current Task has been terminated....
On my second attempt, I opened the object explorer and to view the lf, thinking that might somehow initialize it. I also tried 'recalculate.' After trying to open CodonMutation...bf I got:
Quote:DataSet/DataSetFilter filteredData has not been initialized
Current BL Command:Harvest Frequencies into matrix observedCEFV from DataSet filteredData with unit size = 3 with atom size = 3 with position specific flag = 0 Partition: Current Task has been terminated. Would you like to see the remaining error messages, if there are any?
Clicking 'yes,' I get the same second message as before.
Am I missing something obvious?
For this analysis I'm working with HyPhy on Windows.
Sarah