Figure 3.

Trees NS and NA, confidence intervals and SPR modifications. Subtree pruning and regrafting (SPR) modifications that the NA tree proposes on the NS tree, and the confidence interval around each tree (coloured shapes). Three paths are possible. The labels on the arrows refer to nodes involved in a move: m1 - move outgroup to cluster with hk1774, m2 – move hk1073 to cluster with hk1774, m2r – reverse of m2, m3 – move hk1073 to cluster with outgroup, m4 – move env99 to cluster with quail99/sh39/hk1073 group. t1 - t6 are trees resulting from applying these SPR modifications to the NS tree. Arrows between two trees in the same confidence interval (CI) reflect trivial differences (e.g. m1, black arrow), whereas ones between trees from different CIs are considered significant (e.g. m2, red arrow). We consider m2 as significant as we’re interested in the minimum amount of significant branch moves between NS and NA.

Svinti et al. BMC Evolutionary Biology 2013 13:1   doi:10.1186/1471-2148-13-1
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