WebPhy is a vital web application for phylogenomic analysis, featuring a user-friendly interface that simplifies various tasks, including file format conversion, sequence alignment, tree reconstruction, model selection/validation, and species tree construction. The web server's tools are particularly valuable in scenarios where gene trees within a species exhibit disagreement, addressing systematic challenges related to variations in gene trees, such as differences in topology and branch length. The diverse outcomes generated by the web server are crucial for formulating hypotheses to distinguish between incomplete lineage sorting and other biological processes like hybridization, gene duplication/loss, and horizontal gene transfer.