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This may explain why proteins evolving with an intermediate rate provide the most robust tree.
The complete mtDNA genome-based phylogeny of the Ursidae incorporates the largest amount of phylogenetically informative sequence-based characters and provides the most robust tree for this carnivore family in terms of resolved topology and support for nodes.
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Analyses of the simulated data resulted in the most robust trees, as assessed by the bootstrap, when secondary structure data were included in the phylogenetic reconstruction [68].
We conclude that the presented MrBayes tree is the most robust and most accurate tree out of all calculated trees (Parsimony, distance based, maximum likelihood and MrBayes tree) and therefore we choose this tree as our reference tree in this studied case.
Figure 5A presents the numerical results obtained while considering the noise as a single additional cluster: DBC454 is clearly the most robust method, but ESPRIT-Tree also achieves a good robustness for some intermediate tree-depth values.
Based on previous analyses of actiniarian DNA sequences (e.g., [23] [25]) and studies in other taxa [28], [37], we expect the most robust and well-supported tree to result from such an analysis.
A recent study of chickadee phylogenetics [ 7] found that among several coalescent-based species-tree inference methods, *BEAST was the most robust and consistently converged on the same tree estimated from the authors' full dataset (40 loci) when using 15 loci.
DBC454 was the most robust, closely followed by ESPRIT-Tree.
Noticeably, etr-04 was previously shown to be one of the most robust partitions produced by ESPRIT-Tree (Fig. 5).
The most robust method would require running phylogenetic trees on each OMIM gene, which is not currently a tractable approach on a large, multiple gene family scale because each tree is sensitive to the selection of a suitable set of gene sequences (including outgroups) and must be interpreted manually.
We believe that it will be necessary to look beyond the most commonly utilized sources of data (nuclear ribosomal and mitochondrial sequences) to obtain a robust tree in the future.
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