RogueNaRok output

RogueNaRok output

RogueNaRok writes the results of the rogue taxon search into RogueNaRok_droppedRogues.runId. This file consists of the following columns:

1. num: iteration number of the algorithm (0 means no rogues have been pruned)
2. taxNum: taxon number
3. taxon: taxon name (possibly more than one, for -s > 1)
4. rawImprovement: This is the accumulated support improvement in the consensus tree, if all taxa of the current iteration are pruned (given that all taxa of previous iterations are pruned as well). This value can mean many things: 1.0 for instance could indicate that either one bipartition with support 100% was recovered or that 2 bipartitions with each 50% were recovered or that the support of 3 existing consensus bipartitions was improved by 33% each.
5. RBIC: The RBIC optimality for the reduced consensus tree, after pruning the taxa from the current iteration and all previous iterations.