Distribution of homoplastic sites for the mitochondrial atp6 gene of squamata (2047 positions, above) and for 18S RNA of Coleoptera from an analysis of  (684 positions, below). In terms of quality, the two data sets are very different. While the majority of sites in atp6 are parsimony informative and approximately one third of the sites have a reliability score above qcutoff = 0.8, this is clearly not the case for the data set by  where most of the sites are constant or unreliable. The black bar below the alignment indicates whether the q-value of the corresponding position is above (upper half) or below (lower half) the cutoff value. Note that only green positions have a chance to having q-value above the cutoff value.