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Resolution within the carcharodontosaurids remained the same as the previous analysis [18] with Neovenator remaining the basal-most taxon and high bootstrap values supporting the carcharodontosaurid clades.
The low bootstrap values supporting the Plant II subfamily are due both to the intrinsic high heterogeneity of the sequences of this group and to the presence of a particularly divergent sequence from the green alga Micromonas pusilla (Accession number ACCP01000105.1).
Bootstrap values supporting the topology with the highest maximum likelihood were obtained using Phylip (Felsenstein, 1989).
As above, phylogenetic analysis showed that the Citrus and Arabidopsis proteins clustered together, with high bootstrap values supporting the clade.
Bootstrap values supporting the branches of the tree are rather low; this is to be expected given the diversity of the protein kinase family.
The bootstrap values supporting the clades corresponding to types III, V, VI, VII, VIII and IX are high, respectively 77, 100, 78, 95, 72 and 100.
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High bootstrap values support the existence of the node between the two clusters.
High bootstrap values support the clustering of A/crested eagle/Belgium/01/2004 together with strains from the current Asian H5N1 epidemic.
Our analysis of mitochondrial genomes shows that in most instances the calculated probabilities (ML-mapping, Bayesian posterior probabilities, or bootstrap values) support the expected tree topologies, albeit with surprisingly strong support values.
This conclusion is further supported by the phylogenetic analysis carried out using all available teleost Nme sequences regardless of the genome sequencing status of the species [See Additional file 4] in which high bootstrap values support the Nme3 branch.
While high bootstrap values supported the monophyletic evolution of the V. dahliae Tc1/mariner and Mule elements, the Copia VdLTREs 1 and 5 and the VdHATs fell into distinct lineages.
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