Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t(4)), instead of the O(t(3)) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.