Hello HyPhy team,
I'm analysing complete mitochondrial genomes in birds. I have 41 mitogenomes for 3 different species + 2 outgroups I want to concentrate the analysis to fixed changes, those that occurred in the lineages branches, rather than terminal branches. Should I then reduce the dataset to 1 sequence per lineage? For the whole dataset SLAC/FEL identifies many >1 w codons, but not significant. MEME identifies 24 sites that are under diversifying selection, but most of them are in terminal branches or the outgroups.

I hope all these make sense,

Thanks in advance,

Hernan