The 539-locus concatenated data set in interleaved nexus alignment format from "Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)." The alignment contains 605,087 bp for each of 26 in-group turtle species and two outgroup species (Alligator mississippiensis and Gallus gallus).