Replicating the methodology described by Ding et al. on the capacity of VAEs to delineate phylogenetic relationships among proteins, we confirmed these relationships for our HLD I-IV dataset (Model 1). We observed a star-like configuration, with multiple spikes radiating from a central point in various directions (Fig. ). This pattern indicates that sequences within distinct latent space clusters tend to aggregate if they share a common lineage at a specific evolutionary juncture on the phylogenetic tree. Furthermore, our study confirmed that as sequences evolve from the root to the leaves of the phylogenetic tree, their latent space coordinates move from near the origin to the periphery (Fig. ). Leveraging these observations, we posited that the coordinates within the latent space could serve as a navigational tool in the search for ancestral-like sequences within the sequence space, potentially improving query protein stability while preserving its function.