A pattern recognition-based approach for phylogenetic network construction with constrained recombination

Authors:
M. A. H. Zahid;Ankush Mittal;R. C. Joshi
Affiliations:
Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, India;Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, India;Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, India
Venue:
Pattern Recognition
Year:
2006

Citing 4
Cited 1

Reconstructing a history of recombinations from a set of sequences

SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
Efficient algorithms for lateral gene transfer problems

RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
The Fine Structure of Galls in Phylogenetic Networks

INFORMS Journal on Computing
Pattern recognition techniques for the emerging field of bioinformatics: A review

Pattern Recognition

Counting Faces in Split Networks

ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications

Quantified Score

Hi-index	0.01

Visualization

Abstract

The tree representation of evolutionary relationship oversimplifies the view of the process of evolution as it cannot take into account the events such as horizontal gene transfer, hybridization, homoplasy and genetic recombination. Several algorithms exist for constructing phylogenetic networks which result from events such as horizontal gene transfer, hybridization and homoplasy. Very little work has been published on the algorithmic detail of phylogenetic networks with constrained recombination. The problem of minimizing the number of recombinations in a phylogenetic network, constructed using binary DNA sequences, is NP-hard. In this paper, we propose a pattern recognition-based O(n^2) time approach for constructing the phylogenetic network, where n is the number of nodes or sequences in the input data. The network is constructed with the restriction that no two cycles in the network share a common node.