Figure 9.

Rooted consensus trees of phylogenetic inference strategies averaged over outgroups and species tree construction methods. For a given subset of the 72 phylogenetic inference strategies considered in this article, the bootstrap support for each of the clades that appeared in at least one tree was averaged over the set of strategies to create a set of counts for each of the clades. Greedy consensus trees [12] were then created using the clade counts in the set. Each clade count in the set has a maximum value of 1000, because each element of the set is an average over values that each have a maximum of 1000. These trees disregard branch-length information. (A) Trees constructed using the 18 strategies that utilize ML; (B) MP; (C) NJ; (D) M.