EntroPhylo: An entropy-based tool to select phylogenetic informative regions and primer design

We present a novel entropy-based computational tool that selects phylogenetic informative genomic regions associated with degenerate primer design. This tool identifies proper phylogenetic markers and proposes suitable degenerate primers to amplify and sequence them. The algorithm calculates the entropy value per site, and the selected region is used for primer design. In order to evaluate the tool, sequences of bovine papillomavirus L1 gene were obtained. Once the molecular region was selected, the primers were designed by the software and used in a PCR reaction for viral detection. Three positive samples were tested with four different concentrations, and it was possible to detect the virus in all samples. The results show the applicability of a tool that can select informative regions for phylogenetic analysis and design primers to amplify and sequence these regions, becoming relevant for several studies focusing on pathogen detection, as well as phylogenetic and genetics studies of populations.