We present an easy protocol for evolutionary analysis of proteins, with an emphasis on studying the evolutionary dynamics of disordered regions. Using the p53 protein family as an example, we provide a guide for finding homologous sequences in a database and refining a dataset before constructing the evolutionary context by building a phylogenetic tree. We show how a multiple sequence alignment and phylogeny for a protein family can be further partitioned into smaller datasets in order to investigate the changes in disorder content across the phylogeny. Based on the evolutionary context, we also investigate site-specific conservation of disorder. Last, we address how to evaluate the evolutionary dynamics of disorder-to-order transitions.
Keywords: Conservation; Evolution; IDP; IDR; IUPred; Phylogenetic tree; Protein; Protein family.