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Partitioned Bremer support (PBS) across the 100 nuclear markers in combined Bayesian analyses was used to evaluate the contribution of individual marker to the overall support for the tree (summarized in Appendix S7).
A ML tree summarizing the phylogenetic results is presented in Figure 2.
A decision tree summarizing this paper's findings is presented in Figure 1.
A consensus tree summarizing the tree topologies with higher likelihood based on each data set is shown in Fig. 4b.
We devised a simple decision tree summarizing our results as a guide for treating HER2+ disease with these agents.
The maximum clade credibility (MCC) tree summarizing the trees found from the analysis using 16 calibration points is shown in Figure 1 (and Additional file 2: Table S1).
This "species tree" included all species from which the analyzed spidroin genes were sampled and is a composite tree, summarized from published phylogenies.
In this paper, we provide a polynomial-time algorithm (O(n) where n is the number of species) to calculate the probability of a ranked gene tree topology given a species tree, summarized in Section 'An algorithm'.
These calibration analyses were run for 500,000 generations, sampling the chain every 100 generations, using a 50% majority rule consensus tree summarized from the Markov chains of the Bayesian phylogenetic analysis; the first 50,000 generations were discarded as burn-in.
However, the ML tree (summarized in Figure 4) and several topologies with alternative branching patterns among at the basal-most nodes are statistically indistinguishable under maximum likelihood (Table 4).
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