Minimum-flip supertrees: complexity and algorithms

Author

Duhong Chen ; Eulenstein, O. ; Fernandez-Baca, D. ; Sanderson, M.

Author_Institution

Dept. of Comput. Sci., Iowa State Univ., Ames, IA

Volume

3

Issue

2

fYear

2006

Firstpage

165

Lastpage

173

Abstract

The input to a supertree problem is a collection of phylogenetic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in the input. This task is complicated by inconsistencies due to errors. We consider the case where the input trees are rooted and are represented by the clusters they exhibit. The problem is to find the minimum number of flips needed to resolve all inconsistencies, where each flip moves a taxon into or out of a cluster. We prove that the minimum-flip problem is NP-complete, but show that it is fixed-parameter tractable and give approximation algorithms for special cases

Keywords

biology computing; computational complexity; genetics; molecular biophysics; statistical analysis; trees (mathematics); NP-complete problem; clusters; complexity; fixed-parameter tractable problem; minimum-flip supertrees; phylogenetic trees; taxon; Approximation algorithms; Assembly; Bioinformatics; Clustering algorithms; Error correction; Evolution (biology); Genomics; Geoscience; Materials requirements planning; Phylogeny; NP-completeness.; Phylogenetic tree; supertree; tree assembly; Algorithms; Computational Biology; Evolution, Molecular; Models, Genetic; Phylogeny;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2006.26

Filename

1631997