| Article ID | Journal | Published Year | Pages | File Type |
|---|---|---|---|---|
| 5918993 | Molecular Phylogenetics and Evolution | 2015 | 12 Pages |
•An implementation of IterPCR (Pol and Escapa, 2009) is now available in TNT.•It uses a simple and fast method for checking triplets (LSI or PC).•The method is much faster than Phyutility (Smith and Dunn, 2008).•LSI in RogueNaRok (Aberer et al., 2013) is much slower because it uses quartets.•The optimality criterion in RogueNaRok may fail to detect problematic taxa.
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(t4), instead of the O(t3) 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.
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