Figure S1. Loci statistics boxplots for data derived from [1].

For each locus, the plots illustrate the distributions of (from top to bottom) per-position entropy, per-position gap score [4], per position conservation score [4], sequence length and GC content. 1. Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc R Soc B. 2014;281: 20140970. 2. Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci. 1981;53: 131–147. 3. Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 1994;11: 459–468. 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25: 1972–1973.