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Rather than modeling the trees, she abstracts them to bring out their rhythmic patterns.
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SEB modeled the tree structure and had primary responsibility for writing the manuscript.
To avoid using inconsistent models, the trees inferred from different codon positions and the data sets with gnetophytes removed were constructed under the same tree-building criteria and models as mentioned earlier.
Compared to spectral data, ALS data models the tree size related information better.
The ML function pml returns an object of class pml containing all the information about the model, the tree and data.
The best-fit models of the trees were selected by ProtTest 3.0 [57].
Finally, sitewise rates were calculated with the data sets, the models and the trees as input.
The 'two tree' model was identical to the 'one tree' model, except the tree topology was also unlinked, allowing tree-space to be separately explored for each data partition.
All the analyses assumed a single stationary model across the tree.
The number of allowed base frequency categories (models) along the tree was also fixed.
lnL = log likelihood value for model given the tree, dataset, and parameter estimates.
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