The Site/Group Extended Data format and tools

Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups or residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of these evolutionary patterns requires combining the results of these analyses and mapping them onto molecular structures, a complex task involving distinct coordinate referential systems. To ease this task, we introduce the site/group extended data (SGED) format, a simple text format to store (groups of) site annotations. We developed a toolset, the SgedTools, which permits SGED files manipulation, creating them from various software outputs and translating coordinates between individual sequences, alignments, and three-dimensional structures. The package also includes a Monte-Carlo procedure to generate random site samples, possibly conditioning on site-specific features. This eases the statistical testing of evolutionary hypotheses, accounting for the structural properties of the encoded molecules.