NRM (non-reversible model)

Results file

Results summary

The best-fitting model (based on AIC-c) is .

Based on the comparison of the general reversible (GTR) and non-reversible models (NREV12), there for the non-reversibility of the evolutionary process.

Based on the comparison of the non-reversible model which estimate root character frequencies (NREV12+F) and the model which assumes that these equal empirical frequencies (NREV12), there for the difference in root character frequencies from the distribution implied by the sequences.

Table 1. Summary of model fit, overall tree lengths (subs/site), and corresponding equilibrium frequencies (EF) for each model. Note that the GTR model has the same EF as the base composition of the underlying dataset (empirical frequencies).

Table 2. Rate matrix (Q) for the substitution model . The A⇆G rate is used as the reference (=1.0) for identifiability.

Figure 1. Compare branch length estimates by model (note that because GTR is not able to properly estimate the relative branch lengths of root descendants, the plot excludes those two branches)

Figure 2. Phylogenetic tree renderings show branch lengths under the selected model, and also how the selected measure of differences in base frequencies evolves over the tree. Node bubbles show the difference between the model induced base frequencies and the frequencies observed in the corresponding sequence.

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