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Bootstrap resamplings were carried out 1000 times.

For RAxML trees, 100 bootstrap resamplings were used to estimate confidence of the inferred topology.

Only 100 bootstrap resamplings were performed on this dataset because of its large size (354 homeodomains).

Using CLANN 3.0.3b1, 100 bootstrap resamplings were also carried out on the input data.

Non-parametric bootstrap resamplings were performed to evaluate the robustness of tree topology.

For NJ and UPGMA trees, Poisson correction for amino acid sequences and 10,000 bootstrap resamplings were used, while the Jones, Taylor, and Thorton (JTT) model for amino acid sequences and 100 bootstrap resamplings were used in ML analysis.

Phylogenetic reconstructions were built according to the neighbor-joining method, and 1,000 bootstrap resamplings were performed to assess tree topology (MEGA version 2.1) (2.1.

Bootstrap values were drawn on the best-scoring GARLI ML.

Bootstrap samples were drawn with replacement (100 replications) from the full data set.

In each resampling step, spike responses of randomly chosen units were drawn based on the measured firing probabilities, and the log-likelihood function was computed for each neuron.

NJ trees were drawn with ClustalW [ 48] and bootstrapped 1000 times.