Molerate foreground assignment

[qitingcai]

Hi! I was wondering if there is a way that I could set only internal branches as foregrounds in MoleRate? Thank you!

[spond]

Dear @qitingcai,

At the moment, no. The code will require some terminal branches. The problem with using only internal branches is that they are "fragile". When you run a large genome screen (MoleRate usecase), not all genes will have all species, and the trees will not be identical. Thus, whereas leaf names can always be interpreted without ambiguity, different alignments might have different internal configuration.

Can you explain your use case? I may be able to suggest something.

Best,
Sergei

[qitingcai]

Thanks for the info Sergei! I am trying to test whether genes correspond to an environmental transition event (internal branches) have evolved faster than the rest. In this case I will be using single orthologs where all species are included (and a concensus species tree).

[spond]

Dear @qitingcai,

I can modify the code (in the next release) to basically "subtract" the leaves. That should work. Let me keep this issue open.

Best,
Sergei

[qitingcai]

Thank you Sergei Appreciate it!

Tina