These are the files used for the tree simulations shown in Figure 2A that show converging QC values with increasing replicates. See Appendix S1 for additional details. Contents: INPUT FILES: tree50_TRUE.phy: PHYLIP-format alignment for the 50 taxon tree tree100_TRUE.phy: PHYLIP-format alignment for the 100 taxon tree tree500combined_TRUE.phy: PHYLIP-format alignment for the 500 taxon tree (concatenated test) tree500partitioned_TRUE.phy: PHYLIP-format alignment for the 500 taxon tree (partitioned test) tree500partitioned.prt: RAxML-style partition file for the 500 taxon partition test tree50.tre: Newick-format tree for the 50 taxon tree tree500.tre: Newick-format tree for the 100 taxon tree tree500.tre: Newick-format tree for the 500 taxon tree example.sh: Shows how the script was run using for the 100-taxon tree OUTPUT FILES: node_39_#reps.csv: output file for # of reps for branch QS39 in the 50 taxon tree node_63_#reps.csv: output file for # of reps for branch QS63 in the 100 taxon tree node_489_#reps.csv: output file for # of reps for branch QS489 in the 500 taxon tree See the QS manual for information on the output columns