originally expected. It appears that the selection of particular method and evolutionary model for the analysis is essential. Contrary to previously introduced substituional models based on an the assumption that all sites of the protein undergoes the same substitution process during evolution, the Bayesian mixture CAT model allows to describe distinct substitution processes at the amino-acid replacement occurring in different sites of a protein alignment [26] . In addition to that, CATBP model takes also heterogeneity among sequences (not sites only) into account [27] , which makes it more suitable for the phylogenies that are affected by the compositional bias of the sequences and deals very well with LBA. Indeed, the usage of this model led to even better supported placement of the diatom nuclear psb28 genes compared to CAT model (see Figure 3 for details). All in all, it appears that Bayesian inference with advanced CAT and CATBP models computed tree in agreement with the endosymbiotic gene transfer hypothesis, while all other methods used did not solved the phylogenetic position of diatom nuclear psb28 genes at all. It may not be overlooked that Psb28 is a very short protein containing 112 computable amino acid residues in the dataset matrix, from which only 82 characters are parsimony informative. The limited length of the analyzed gene consequently leads to lower or even no support of particular nodes in the tree, especially when the dataset contain high number of OTUs. Moreover, since the dataset contain also highly divergent sequences, phylogenetic information should