Generalized tree alignment
In computational phylogenetics, generalized tree alignment is the problem of producing a multiple sequence alignment and a phylogenetic tree on a set of sequences simultaneously, as opposed to separately. Formally, Generalized tree alignment is the following optimization problem. Input: A set  and an edit distance function  between sequences,

Output: A tree  leaf-labeled by  and labeled with sequences at the internal nodes, such that  is minimized, where  is the edit distance between the endpoints of . Note that this is in contrast to tree alignment, where the tree is provided as input. References

Computational phylogenetics