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

P. GOLOBOFF; C. SZUMIK

MOLECULAR PHYLOGENETICS AND EVOLUTION

ACADEMIC PRESS INC ELSEVIER SCIENCE

Lugar: Amsterdam; Año: 2015 vol. 88 p. 93 - 104

1055-7903

This paper describes an efficient implementation of triplet-based measures of stability, inthe program TNT. The only available implementations of such measures are much slowerthan the present one, either because of an inefficient implementation (Phyutility, Thor) orbecause the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead ofthe O(t3) possible for triplets). The method to quickly calculate triplets is applied to solvingIterPCR (Pol and Escapa 2009). It is shown that, in some cases, IterPCR or otheralgorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves)produce more informative results than analysis with RogueNaRok.