Unrooted gene trees for big gene families

[Jacopo Martelossi]

Hi everyone,

I was wondering if GeneRax can give reasonable results even when dealing with big gene families with many duplications, even before the specie tree root. As far as I understand from the documentation, the given gene tree can be unrooted but its root position can greatly affect final results, I suppose. Is it still a good idea to use GeneRax in these situation or is it better to split gene families into, for example, orthogroups?

Thanks in advance,

Jacopo

[Benoit Morel]

Dear Jacopo,

Sorry for the late reply, I am currently on vacations.

I don't think that having duplications before the species tree root is an issue. The gene tree root position matters, but the exact position among all internal nodes that correspond to duplications before the species tree root should not matter (and can't be inferred).

I don't think that you need to split gene families, unless:

- the inference is too slow (it should get faster with more but smaller gene families)

- you expect that splitting the gene families could improve the sequence alignment quality

In general, I think that both approaches (splitting or not) are correct, and I don't expect one to be better than the other. You could try both and see if you find consistent results.

I hope it helps!

Benoit