A consensus tree provides an estimate for the level of support for each clade in the ﬁnal tree. It is built by combining clades which occurred in at least a certain percentage of the resampled trees. This percentage is called the consensus support threshold. A 100% support threshold results in a Strict consensus tree which is a tree where the included clades are those that are present in all the trees of the original set. A 50% threshold results in a Majority rule consensus tree that includes only those clades that are present in the majority of the trees in the original set. A threshold less that 50% gives rise to a Greedy consensus tree. In constructing a Greedy consensus tree clades are ﬁrst ordered according to the number of times they appear (i.e. the amount of support they have), then the consensus tree is constructed progressively to include all those clades whose support is above the threshold and that are compatible with the tree constructed so far.
The length of the consensus tree branches is computed from the average over all trees containing the clade. The lengths of tip branches are computed by averaging over all trees.
Note: The above deﬁnitions apply to rooted trees. The same principles can be applied to unrooted trees by replacing “clades” with “splits”. Each branch (edge) in an unrooted tree corresponds to a diﬀerent split of the taxa that label the leaves of this tree.