noisy noisy .(A) The fraction of sites marked as randomized depend on the cyclic ordering. Phylogenetically reasonable ordering such as those computed by NeighborNetNeighborNet, QNetQNet, or from the guide tree of the alignment program ClustalWClustalW have a nearly minimal fraction of putative randomized alignment sites. (B) The average bootstrap support increases for moderate values of q i.e., as long as not too large a fraction of alignment columns are removed. The effect increases with the size of the data set. (C) Distributions of randomized positions can differ substantially between data sets, here 18S RNA of Coleoptera (l.h.s.) and mitochondrial atp6atp6 gene of squamata (r.h.s.). Red indicates randomized positions, light red singletons, green parsimony informative sites. The bars below indicate included and excluded parts of the alignment, respectively. (Adapted from ).