Comparative Analysis of Fungal Phylogenetic Trees and Genetic Distances Using PROST and Traditional Methods. A) a phylogenetic tree generated using PROST’s distance metric between species in the BUSCO set of proteins without the need for an MSA. This tree was generated by neighbor-joining method from the PROST distance matrix. B) a phylogenetic tree created using traditional methods, specifically, by concatenating the MSA of the BUSCO set of orthologs and calculating distances with Phylip (Weisman et al., 2020). Both trees display a notable similarity in topology, particularly highlighting the yeast lineage (shaded in yellow), which encompasses Saccharomyces species. C) comparison of the phylogenetic distances obtained by both methods across various yeast species, indicating a strong correlation between the PROST distances (orange line) and those derived from traditional phylogenetic analysis (blue line). The distances parallel each other and are similar, suggesting that PROST can effectively approximate the genetic distances typically obtained through more computationally intensive methods. Here the distance between a pair of organisms is calculated by taking the average PROST distance summed over all BUSCO proteins.