## The Deferred Path Heuristic for the Generalized Tree Alignment Problem (1997)

Venue: | JOURNAL OF COMPUTATIONAL BIOLOGY |

Citations: | 11 - 3 self |

### BibTeX

@INPROCEEDINGS{Schwikowski97thedeferred,

author = {Benno Schwikowski and Martin Vingron},

title = {The Deferred Path Heuristic for the Generalized Tree Alignment Problem},

booktitle = {JOURNAL OF COMPUTATIONAL BIOLOGY},

year = {1997},

pages = {257--266},

publisher = {Press}

}

### Years of Citing Articles

### OpenURL

### Abstract

Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a phylogenetic tree, a structure frequently being predicted only after the multiple alignment instead of together with it. The Generalized Tree Alignment problem addresses both questions simultaneously. It can formally be viewed as a Steiner tree problem in sequence space and our approach merges a path heuristic for the construction of a Steiner tree with a clustering method as usually applied only to distance data. This combination is achieved using sequence graphs, a data structure for efficient representation of similar sequences. Although somewhat slower in practice than an earlier method by Hein (Mol. Biol. Evol., 6:649--668,1989) the current approach achieves significantly better results in terms of the underlying scoring function. Furthermore, a variant of the algorithm is intr...