Figure 4.

Dependency of tree-quality indices on the cut-off value q_cutoff 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) [27], and the rescaled consistency index (RC) [28] as computed by PAUP 4.0b10 [26]. 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.