Screenshot showing the Nexplorer interface with intron data for a subset of the ATP Synthase Subunit C family, with control panel (above), data matrix (right), and gene phylogeny (left). The pop-up menu shows node-specific operations. Taxonomic coloring (key, upper right) reveals sub-trees representing paralogous sub-families, each with genes from plants, animals, fungi and protists (custom color schemes can be applied based on user-defined sets in the input file, which will appear automatically in the “Set Coloring” box). The data matrix shows the presence (“+”) or absence (“.”) of introns at the 19 positions listed above the matrix in codon-phase notation (e.g., “30-1” indicates codon 30, phase 1). The red numbers at nodes are branch support values (here, Bayesian posterior probabilities). This screenshot shows interface elements but has limited resolution: for unlimited resolution, the user may select PostScript instead of “Clickable (PNG)”.