Tree Alignment (TA) and Generalized Tree Alignment (GTA):

An MSA is constructed with respect to a phylogenetic tree, which can be specified (TA) or is constructed (GTA) [36,30,21,31]. First the sequences at the leaves are aligned in a pairwise manner. Then in the next step either a representative sequence is calculated or a probabilistic ancestral sequence is determined. The drawback here is that the correct evolutionary tree is needed, something which is typically not available. We note that the calculation of evolutionary trees is also still an open problem mainly due to the fact that the problem is NP-complete [8].