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 S {\displaystyle S} and an edit distance function d {\displaystyle d} between sequences,

Output: A tree T {\displaystyle T} leaf-labeled by S {\displaystyle S} and labeled with sequences at the internal nodes, such that Σ e ∈ T d ( e ) {\displaystyle \Sigma _{e\in T}d(e)} is minimized, where d ( e ) {\displaystyle d(e)} is the edit distance between the endpoints of e {\displaystyle e} .

Note that this is in contrast to tree alignment, where the tree is provided as input.