Parsimony analysis of phylogenomic datasets (I): Scripts and guidelines for using TNT (Tree Analysis using New Technology)
- Torres Galvis, Ambrosio
- Goloboff, Pablo Augusto
- Catalano, Santiago Andres
DOIAbstract
We discuss here the use of TNT (Tree Analysis using New Technology) for phylogenomic analysis. For such data, parsimony is a useful alternative to model-based analyses, which frequently utilize models that make unrealistic assumptions (e.g. low heterotachy), struggle with high levels of missing data, etc. Parsimony and model-based methods often yield trees with few topological differences, which can then be analyzed further in order to investigate whether these few topological differences are due to undesirable analysis artefacts. This is facilitated by the greater speed and computational efficiency of parsimony, which allow for a more in-depth analysis of datasets. We here briefly describe the computationally most efficient and versatile p...
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