Dependency of tree-quality indices on the cut-off value q
for the protein-coding mitochondrial genes from all 31 currently available squamata. The stability of the trees is measured by the scaled log likelihood (ln L)/n, the homoplasy index (HI) , and the rescaled consistency index (RC)  as computed by PAUP 4.0b10 . Data sets are alignments (supplied in the electronic supplement) of individual mitochondrial protein-coding genes. They vary in size (from about 170 to 1800 nt) and randomization.