RBIC

The optimality criterion optimized by RogueNaRok is the relative bipartition information criterion (RBIC). It is the proportion of the maximum possible support a fully bifurcating consensus tree with the initial taxon set could have, if all bipartition in this consensus tree were fully supported (i.e., 100% support).

In other words to score the RBIC optimality of a consensus tree, we add up all support values on branches in this consensus tree and divide by (n-3), where n is the number of taxa in the initial bootstrap trees.

By comparing the initial RBIC and the RBIC after pruning rogue taxa, we can assess by how much the support of consensus bipartitions could be increased. Of course, as soon as we prune taxa, it becomes impossible for the reduced consensus tree to attain an RBIC optimality of 100%.

Be aware of this fact that the RBIC is always relative to the number of taxa in the initial taxon set. A note on comparability: Assume you conduct an analysis with 100 taxa and pruning 5 rogue taxa improves the RBIC from 53% to 58%. Then you remove the 5 rogue taxa from the alignment, conduct a de novo bootstrap analysis and run RogueNaRok again. Assume you find 1 rogue taxon, that improves the RBIC from 60% to 61%. The point is that the pairs 53%/58% and 60%/61% are not comparable to each other, since the first pair is relative to 100 taxa and the second pair is relative to 95 taxa. Instead you can compare the raw sum of support, e.g. 60%95 to 53100.