Abstract
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. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a Reciprocal Best Hit based method, while achieving equal or better accuracy.