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Bootstrap percentage values are shown in Additional file 4: Figure S2.
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Bootstrap percentage values greater than 50% are given at the nodes of the tree (1000 replicates).
Phylogenetic trees were constructed by using the neighbor-joining method; data were resampled 1,000× to generate bootstrap percentage values.
In each of the phylogenetic tree, bootstrap percentage values that showed a stability of at least 80% were considered.
Bootstrap percentage values (50%) generated from 1,000 replicates from maximum parsimony and posterior probabilities (>80%) from Bayesian analysis are shown as [Maximum parsimony bootstrap value/Bayesian posterior probabilities].
Phylogenetic analysis of promoter regions was performed as described above, and percentage of bootstrap values are shown at branches.
Bootstrap support values are indicated on branches.
Bootstrap supporting values are indicated.
For orthology detection methods, bootstrap values are calculated as the percentage of bootstrapped trees in which two sequences are identified as orthologs, i.e. a confidence measure for orthology prediction.
Bootstrap values are reported as percentages and indicate how often a cluster was observed in the bootstrapping.
Bootstrap values are expressed as percentages.
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