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.
Famous quotes containing the words generalized and/or tree:
“One is conscious of no brave and noble earnestness in it, of no generalized passion for intellectual and spiritual adventure, of no organized determination to think things out. What is there is a highly self-conscious and insipid correctness, a bloodless respectability submergence of matter in manner—in brief, what is there is the feeble, uninspiring quality of German painting and English music.”
—H.L. (Henry Lewis)
“The windy springs and the blazing summers, one after another, had enriched and mellowed that flat tableland; all the human effort that had gone into it was coming back in long, sweeping lines of fertility. The changes seemed beautiful and harmonious to me; it was like watching the growth of a great man or of a great idea. I recognized every tree and sandbank and rugged draw. I found that I remembered the conformation of the land as one remembers the modelling of human faces.”
—Willa Cather (1873–1947)