This study does not examine phenotypes, but may be applied to them somehow. Instead:
>we use simulation to show that CNNs can leverage images of aligned sequences to accurately uncover regions experiencing gene flow between related populations/species, estimate recombination rates, detect selective sweeps, and make demographic inferences
I believe this works well because the sorting of the data (Fig. 2) introduces phylogenetic information into the image to be analyzed. This reminds me of neighbor joining [0], but has some differences. Without this ordering, their method does not work as well.