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The branching pattern and bootstrap support does not show a clear affinity with either eIF4E-2a or -2b, but based on sequence length, the Amoebophrya eIF4E-2 was more similar to eIF4E-2a.
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Consistent branching patterns and bootstrap support values also depict distinct groupings among paralogs for vertebrate protein families (fig. 5).
Figure 4 shows representative NJ trees of both the ITS-rDNA and NaGIR2 phylogenies with overall congruent branching patterns and significant bootstrap and Bayesian supports.
The overall pattern of bootstrap support in our ML analyses is that families and divergences within them are generally strongly supported; superfamilies and divergences within them are only sometimes strongly supported; and relationships among superfamilies almost always have very weak support, with bootstraps often < 20% (see Additional files 4 and 7).
Special topics: cross-fold validation and bootstrap inference.
We evaluated information bias combining quadratic estimation and bootstrap subtraction59.
1000 iterations were conducted for bootstrap support, and bootstrap values are indicated at each node.
The branch supporting this pattern received bootstrap support of 90%.
The phylogenetic analysis of the U3 sequences yielded a significant branching pattern with bootstrap values of greater than 50.
For example, the MP-EST consensus tree for the mammal data set has high bootstrap supports for the branches close to the terminal tips and low bootstrap supports for the branches close to the tree root, which is consistent with the pattern of bootstrap values in gene trees (Additional file 3: Figure S3).
Phylogenetic trees obtained from both datasets (mtDNA1 and mtDNA2) and derived from Bayesian inference and the ML algorithm yielded identical tree topologies and mainly well supported branching patterns (ML bootstrap values: 99 100%, Bayesian posterior probabilities: 1.0) (Fig..2).
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