Simulated data with manually introduced SPR modifications. The HA data was simulated on a tree modified by moving taxon ‘G’ to group with taxon ‘B’. (A) Output from the ML analysis for seven segments: MP, NA, NP, NS, PA, PB1 and PB2. A significant SPR was detected that would require moving taxon ‘G’ to group with taxon ‘B’, as suggested by the HA segment (direction of arc from empty to filled circle). Colours of arcs correspond to specific SPR operations. (B) HA tree: seven segments propose a significant SPR modification on the HA tree that would require moving taxon ‘G’ to group with taxon ‘F’. (C) Frequency network from Bayesian results. Edges point from segment proposing an SPR, to the segment whose tree needs to be modified (filled circle). Legend shows SPRs corresponding to the coloured edges. HA proposes moving taxon ‘G’ to group with taxon ‘B’ for the other seven segments. Conversely, the rest of the segments suggest that ‘G’ should move to cluster with ‘F’ on the HA tree. (D), (E) Overlap between MLreassort and Breassort. The x-axis represents the segments that propose the SPR move, whereas the y-axis represents the segments whose trees need to be modified according to that SPR. The name of a tree segment is greyed out in the case where the SPR move is irrelevant, i.e. when the taxa involved in the move are sister-taxa.