Genomic Fishing and Data Processing for Molecular Evolution Research

Molecular evolution analyses, such as detection of adaptive/purifying selection or ancestral protein reconstruction, typically require three inputs for a target gene (or gene family) in a particular group of organisms: sequence alignment, model of evolution, and phylogenetic tree. While modern advances in high-throughput sequencing techniques have led to rapid accumulation of genomic-scale data in public repositories and databases, mining such vast amount of information often remains a challenging enterprise. Here, we describe a comprehensive, versatile workflow aimed at the preparation of genome-extracted datasets readily available for molecular evolution research. The workflow involves: (1) fishing (searching and capturing) specific gene sequences of interest from taxonomically diverse genomic data available in databases at variable levels of annotation, (2) processing and depuration of retrieved sequences, (3) production of a multiple sequence alignment, (4) selection of best-fit model of evolution, and (5) solid reconstruction of a phylogenetic tree.