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For the purposes of this work, we consider it adequate to constrain the topologic comparison only between trees obtained with k-tuple distance methods.
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The incongruence between molecular trees obtained with different methods or different data sets is also frequently encountered [ 23, 24] Studies on several other systems reveal similar uncertainty as we observed in our analysis [ 25, 26].
We compare the different topologies in the search for similar managing patterns, and compare the trees obtained with two simple models of growing networks and with a model that interpolates between them and incorporates the heterogeneity of the computer users.
The BI phylogenetic trees obtained with MrBayes 3.1 [ 44], described previously, were used as input trees.
The trees obtained with the different methods were broadly congruent and a representative tree is shown in Figure 1.
The trees obtained with ML and Bayesian approaches had almost identical topologies.
The trees obtained with PhyML are presented in Figure 2 in Additional file 1.
Additional file 4: Unabridged ML tree obtained with RAxML.
Figures 7A and B presents the ML tree obtained with PHYML and the consensus tree obtained with MrBayes.
The tree obtained with the best model showed little difference with the tree resulting from the consensus of all model.
Furthermore, a candidate tree obtained with a distance method can be taken as a starting tree for ML heuristic searches.
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