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The genotype with maximal posterior probability was picked as the genotype for that locus.
Finally, for each replicate r and strain s, we determined the values w rs that have maximal posterior probability.
Brown et al. [ 12] combine the SSVS approach with another machine learning technique called simulated annealing to instead select one high, preferably maximal, posterior probability model.
Within mollusks, the clades Aculifera and Conchifera received maximal posterior probability support in BI and low (<50%) bootstrap support in the ML analysis.
This clade is the sister group of remaining gastropods with low bootstrap support in ML or of cephalopods with maximal posterior probability support in BI.
Consistent with the difficult positioning of this genus, the supermatrix tree groups it with Hordeum with a rather weak bootstrap support (0.69), although maximal posterior probability (1.00), conflicting with the BUCKy tree.
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However, we note that these nodes all have high or maximal posterior probabilities in BI analyses (Table 1).
A standard measure of the quality of a mixture model fit is the likelihood, which is the product, over all points, of the maximal posterior probabilities.
The resulting Bayesian trees were well resolved: all nodes of the backbone tree and genus crown nodes were recovered with maximal posterior probabilities (PP = 1, Figure 1 and Additional file 2: Figure S1).
The maximal posterior error probability (PEP), which is the individual probability of each peptide to be a false hit considering identification score and peptide length, was set to 0.01.
A Bayesian phylogenetic analysis using the LG model (fig. 1 a) recovered a three domains tree with maximal support (posterior probability of 1 for archaeal monophyly).
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