Species tree vs. gene tree as input

[Anh-Thu-Weber]

Dear Carine,

Thank you for developing this useful tool and for the clear tutorial, I have a comment though;
My understanding is that when possible, we should use a species tree as input (inferred from several loci) and not the focal gene tree (as you also suggest in a response to an issue). Yet in the main tutorial it is mentioned several times to use a gene tree as input (but mention to a species tree is also there) - therefore I got confused the first time I used PCOC and generated & used a gene tree for the gene of interest (although I had a well-resolved species tree). But when available, a species tree should be used, right?
To clarify this, maybe it would be better to use 'species tree' all over the tutorial rather than 'gene tree', or clarify this in 1-2 sentences at the beginning of the tutorial?
Thanks again,

Alexandra