The dataset consists of a PDF file and two plain-text TNT scripts (*.run files). The PDF includes supporting Figures for the additional analyses conducted by Flores et al. on paleontological datasets. The TNT scripts conduct two complementary sets of analyses: (a) evaluation of taxon instability relative to the incompleteness ("mc.run"), and (b) changes in branch support values after pruning unstable taxa ("avmc.run"). To properly run these files in TNT, the name of the matrix files should be given as arguments (see the TNT documentation webpage for details on the usage of script files). The scripts generate CSV-formatted output for being subsequently read into any other software. Script files are provided as "ready-for-use", and are freely distributable and modifiable. We request that you cite the respective paper and dataset.