Hi,

I am new to HyPhy and I have a few basic questions. I am using the GUI interface to estimate branch-by-branch omegas on simulated data (16 taxa, balanced tree, codon model, MG94).

1. When I read the user-defined tree, the tree is correctly read as rooted. However, the tree given by the likelihood optimization is unrooted. Why is that and what effect does it have on the omega estimation of the branches (especially those that are now connected to a basal politomy)?

2. is it possible to calculate confidence intervals on the omega estimates?

3. for now I am using the GUI interface but I know it is possible to use scripts to analyze multiple files. Any easy tutorial to teach me how to do that for this analysis?

Thanks,
fabia

Hi Fabia,


Quote:

1. When I read the user-defined tree, the tree is correctly read as rooted. However, the tree given by the likelihood optimization is unrooted. Why is that and what effect does it have on the omega estimation of the branches (especially those that are now connected to a basal politomy)?

Because the models are time-reversible, rooting should have no effect of the estimates of omegas.


Quote:

2. is it possible to calculate confidence intervals on the omega estimates?

Indeed; through the GUI it can be done following the procedure described on pages 8-10 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Theres is also a thread Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login which should get you started on how to do this in the command line version (or through the GUI version but not using the batch language). This thread should also address your question 3. Code examples in the thread deal with the models where omega varies from branch to branch.

Sergei