I have generated a phylogenetic tree depicting the relationship between PKS domains of 8 fungal species. I am interested in orthologous domain comparison between species and finding gene family contraction/expansion.
What I want to know is what is the best outgroup for this? If I was doing a species tree phylogeny I would just select a fungal species that is related to but distant enough. I am not sure what domain to use for a PKS outgroup.