In computationalphylogenetics,generalized tree alignment is the problem of producing amultiple sequence alignment and aphylogenetic tree on a set of sequences simultaneously, as opposed to separately.^[1]

Formally,Generalized tree alignment is the following optimization problem.

Input: A set${\displaystyle S}$ and an edit distance function${\displaystyle d}$ between sequences,

Output: A tree${\displaystyle T}$ leaf-labeled by${\displaystyle S}$ and labeled with sequences at the internal nodes, such that${\displaystyle {\mathrm{\Sigma }}_{e\in T}d(e)}$ is minimized, where${\displaystyle d(e)}$ is the edit distance between the endpoints of${\displaystyle e}$.^[2]

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

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