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A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction

by Mridu Gupta, Shailendra Singh
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 52 - Number 9
Year of Publication: 2012
Authors: Mridu Gupta, Shailendra Singh
10.5120/8229-1303

Mridu Gupta, Shailendra Singh . A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction. International Journal of Computer Applications. 52, 9 ( August 2012), 14-18. DOI=10.5120/8229-1303

@article{ 10.5120/8229-1303,
author = { Mridu Gupta, Shailendra Singh },
title = { A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction },
journal = { International Journal of Computer Applications },
issue_date = { August 2012 },
volume = { 52 },
number = { 9 },
month = { August },
year = { 2012 },
issn = { 0975-8887 },
pages = { 14-18 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume52/number9/8229-1303/ },
doi = { 10.5120/8229-1303 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T20:51:49.394719+05:30
%A Mridu Gupta
%A Shailendra Singh
%T A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction
%J International Journal of Computer Applications
%@ 0975-8887
%V 52
%N 9
%P 14-18
%D 2012
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution. Different phylogenetic reconstruction techniques are available. In this paper Distance based technique is used. Distance measure is an important issue in phylogenetic analysis. Traditional approaches are time-consuming due to the fact that they require multiple sequence alignment, while the K-tuple distance is easy to compute and has been used in phylogenetic tree reconstruction. Based on this K- tuple distance, a genetic algorithm is proposed to find a new F-tuple distance measure which takes into account the position of occurrence of tuples and instead of considering difference, similarities between the sequences are considered. The K-tuple distance approach is not effective for set of sequences which are almost identical where as F-tuple distance is useful for constructing phylogenetic tree for set of identical sequences. This novel approach is capable of efficiently building phylogenetic trees and is less computational intensive.

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Index Terms

Computer Science
Information Sciences

Keywords

Distance Method Distance Matrix Phylogenetics Phylogenetic Tree K-tuple distance Genetic Algorithm F-tuple distance

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