I'm returning to this task after a two-month hiatus. HyPhy is no longer crashing, but I also can't get CodonMutationToTreeMapper.bf to work using the GUI on my Mac.

Here's what I do:

1. I open a data set, create a partition, select a tree and a model, and set parameters to local. I then build a likelihood function. I save the likelihood function using the gears button, as Sergei suggested. A window pops up asking me if I want to include an optimization step; I say yes. (Should I optimize now instead?)

2. I then open the file to which I saved the likelihood function and change the function's name as Art described to "lf". (I haven't included the code Sergei wrote.)

3. I then select File > Open Batch File and choose CodonMutationToTreeMapper.bf. The GUI terminal window says it's reconstructing ancestors, prints 10410.4 two times on the screen, and a "Dead End" window appears, saying,

"An error occured:
DataSet/DataSetFilter filteredData has not been initialized
Current BL Command:Harvest Frequencies into matrix observed CEFV from DataSet  filteredData with unit size = 3 with atom size = 3 wth position specific flag = 0
Partition:
Curren operation/job has been terminated."

Another "Dead End" window appears, complaining about setupMapToTree(0).

Is there a reference for this bf short of the code itself? Should I scrap the GUI and try command line on Linux?

Thanks so much for your help and patience.

Sarah

Great! It works! I ran AnalyzeCodonData.bf as you suggested and then chose CodonMutationToTreeMapper.bf from the gears button.

I'm thinking I might try to modify the bf so that the tree shows tip labels. I have a hard time reading on which branches the substitutions occur (the branches are also very dense relative to the size of the letters). Is there a way to print substitutions from a range of codons on the tree, rather than the substitutions associated with one residue at a time?

I think it'd be good practice to try to modify the code myself. My goal is to show the (dis)appearance of glycosylation sites on the tree.

Thanks again,
Sarah