Prunier 1.0 (fast version) ran on this gene family whose gene tree is on the left, given the reference species tree on the right. Prunier's conflict threshold was set to 80. Prunier inferred three lateral gene transfers (LGT). Circled nodes correspond to support values of conflicting nodes that are removed when the corresponding transferred group (same color) is pruned from the trees. Colored arrows and squares indicate topological moves that can reconcile the transferred groups position in the two trees.
The two first inferred transfers, #1 and #2 are not significant, since their LGT score is below the threshold. The #1 corresponds to a local conflict, and removing corresponding species can not help to reconcile the two trees by removing the only significantly conflicting node (circled in blue, support of 93). However the conflict produced by the misplacement of "GEKAU1" is not local. Its reference position is at more than one node from its position in the gene tree. Moreover, the conflicting node of 93 support can not be removed by the pruning of a single group. Its conflict is produced by two groups (the blue and the green one), that swapped their position around this node (blue ang green arrows cross)... Finally, the LGT #2 has a non significant score, but is linked to a significant conflict.