Distance matrix with HKY model
Hi!
I am working with a relatively large COI dataset (~3200 sequences). I just ran a ModelTest with my alignment file, and the best model according to BIC is the HKY+G4 (gamma shape=0.3274). My goal is to strictly get a distance matrix for downstream analysis, I'm not interested in building a phylogenetic tree. For this I'm using the ape R package, however in the dist.dna() function there is no HKY model, but there is a F84 model that apparently is equivalent (but still not the same). Is it recommendable to just run the calculations using the F84 model (and adjusting the gamma value) or is there a significant risk by doing this? Should I just use another model that is present in the ape package with a slightly worse score?
Thanks in advance for your insights.