Selecting the branches for an evolutionary tree: a polynomial time approximation scheme

Authors:
Jonathan Badger;Paul Kearney;Ming Li;John Tsang;Tao Jiang
Affiliations:
Department of Computer Science, University of Waterloo, Waterloo, ON N2L3G1, Canada;Department of Computer Science, University of Waterloo, Waterloo, ON N2L3G1, Canada;Department of Computer Science, University of Waterloo, Waterloo, ON N2L3G1, Canada;Department of Computer Science, University of Waterloo, Waterloo, ON N2L3G1, Canada;Department of Computer Science, University of California, Riverside, CA
Venue:
Journal of Algorithms
Year:
2004

Citing 7
Cited 1

A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed

SIAM Journal on Computing
A practical algorithm for recovering the best supported edges of an evolutionary tree (extended abstract)

SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
Computers and Intractability: A Guide to the Theory of NP-Completeness

Computers and Intractability: A Guide to the Theory of NP-Completeness
Constructing Big Trees from Short Sequences

ICALP '97 Proceedings of the 24th International Colloquium on Automata, Languages and Programming
Inferring Evolutionary Trees with Strong Combinatorial Evidence

COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
Two Strikes Against Perfect Phylogeny

ICALP '92 Proceedings of the 19th International Colloquium on Automata, Languages and Programming
Orchestrating Quartets: Approximation and Data Correction

FOCS '98 Proceedings of the 39th Annual Symposium on Foundations of Computer Science

Convex recolorings of strings and trees: Definitions, hardness results and algorithms

Journal of Computer and System Sciences

Quantified Score

Hi-index	0.00

Visualization

Abstract

Many fundamental questions in evolution remain unresolved despite the abundance of genetic sequence data that is now available. This state of affairs is partly due to the lack of simultaneously efficient and accurate computational methods for inferring evolutionary trees. Efficient methods are critical since the abundance of sequence data has resulted in the need to analyze large datasets. Methods with guaranteed accuracy are important since biologists require proof that results are meaningful. In this paper the first polynomial time approximation scheme (PTAS) for selecting the branches of an evolutionary trees from a list of candidate branches is presented. PTAS's are highly desirable since they allow the approximation of an optimal solution with arbitrary precision in polynomial time. This PTAS is based upon recent advances in the approximation of smooth polynomial integer programs.