Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample's protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs.