Hello,

The documentation for Hyphy states that "HyPhy can work properly with any member of the class of general time reversible models, regardless of the number of character states. "

Does Hyphy also work properly for non time reversible models?  Should I force Hyphy to accept a rooted topology when doing this? 

From what I understand, the likelihood will change depending on the rooting when using a nonreversible model.   I am not really interested in the value of the likelihood;  I am more interested in the values of the rate matrix.  Will the rate matrix values also change depending on the root?

Any help you can provide is greatly appreciated.  Thanks.

Jeff

Dear Jeff,

The only fundamental difference in how one goes about computing the phylogenetic likelihood function, when general (non-reversible) models are used, is that the placement of the root is now important, i.e. one can't automatically 'unroot' the tree.

HyPhy will unroot all trees, unless the ACCEPT_ROOTED_TREES batch language
language constant is set to '1'.

I can imagine cases when placement of the root may have a strong effect on rate estimates (e.g. a large tree, where the 'outgroup' is incorrectly rooted to be deep in the tree).

Cheers,
Sergei

Hi Sergei,

Thanks for the quick reply and for the helpful information.

Quote:


This is what I did, but then I got worried when reimporting the batch files and saw the likelihood changing.  I have now stuck the  "ACCEPT_ROOTED_TREES=1;"  code into the batch file as you suggested, and that worked great.  Thanks.


I have another question if you don't mind.  I'd like to estimate the actual number of specific changes that have occurred along a particular lineage.  For example, the number of A->G transitions that have occurred along the human branch subsequent to the split between humans and chimps.  I'm using local rate matrices, so that each branch has its own set of rates.  And the matrices are nonreversible as I've mentioned, so that the A->G rate is separate from the G->A rate.  What would be the best way to go about this?

I tried doing this by first reconstructing ancestral sequences, then taking the number of A's present in the human-chimp common ancestor and multiplying this number by the A->G rate from the human branch matrix.  It seems like this should give me the number of A->G changes that have occurred along the humun branch, but do I need to consider the possibility of multiple changes along the branch?  For instance, some of the A->G changes might actually go A->G->C by the end of the branch.  Do you have any thoughts on whether this approach is valid, and/or any suggestions on how else I could approach this?

Thanks again for your help.

Hi Sergei,

Ahhh well, I was afraid it wouldn't be easy.  I'll look into the references you mentioned and see what I can do.  You've been very helpful.  Thanks a lot.

Jeff