Phylogenomics aims to infer the evolutionary relationships of organisms, and their genomes, genes, and proteins, from genomic data. Understanding the evolution of these components can provide clues about their biological functions. Here we describe minimal protocols for inferring families of genes (and the proteins they encode), and using them in phylogenomic analyses to infer species trees.
Keywords: Fungi; Genomics; MCL clustering; Orthologs; Phylogenetic tree; Phylogenomics; Phylogeny inference; Protein families.