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Reseach Article

A Comparative Study of Multiple Sequence Alignment Tools to Construct Phylogenetic Trees

Published on February 2013 by Farhana Sarkhawas, R.k. Kamat
International Conference on Recent Trends in Information Technology and Computer Science 2012
Foundation of Computer Science USA
ICRTITCS2012 - Number 12
February 2013
Authors: Farhana Sarkhawas, R.k. Kamat
0070b7d9-4188-40ca-835c-33d41b7f2838

Farhana Sarkhawas, R.k. Kamat . A Comparative Study of Multiple Sequence Alignment Tools to Construct Phylogenetic Trees. International Conference on Recent Trends in Information Technology and Computer Science 2012. ICRTITCS2012, 12 (February 2013), 12-14.

@article{
author = { Farhana Sarkhawas, R.k. Kamat },
title = { A Comparative Study of Multiple Sequence Alignment Tools to Construct Phylogenetic Trees },
journal = { International Conference on Recent Trends in Information Technology and Computer Science 2012 },
issue_date = { February 2013 },
volume = { ICRTITCS2012 },
number = { 12 },
month = { February },
year = { 2013 },
issn = 0975-8887,
pages = { 12-14 },
numpages = 3,
url = { /proceedings/icrtitcs2012/number12/10418-1449/ },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Proceeding Article
%1 International Conference on Recent Trends in Information Technology and Computer Science 2012
%A Farhana Sarkhawas
%A R.k. Kamat
%T A Comparative Study of Multiple Sequence Alignment Tools to Construct Phylogenetic Trees
%J International Conference on Recent Trends in Information Technology and Computer Science 2012
%@ 0975-8887
%V ICRTITCS2012
%N 12
%P 12-14
%D 2013
%I International Journal of Computer Applications
Abstract

Phylogenetic tree is a branched structure which represents the evolutionary relationships among genes and organisms. Multiple sequence alignment is an initial step in constructing a phylogenetic tree. The most widely used tools for phylogenetic analysis i. e. PHYLIP (Phylogeny Inference Package) and PAUP (Phylogenetic analysis using parsinomy) have so far been used for inferring phylogenies. However, the above referred packages inturn had to rely on other tools for input. In this context, many open source MSA tools are available for generating both multiple sequence alignment and phylogenetic tree. The purpose of the present paper is to highlight various open source MSA tools for constructing phylogenetic trees using distance based methods after generating the alignment. A comparative study of five MSA tools Geneious, ClustalX, DNAMAN, STRAP and MUSCLE is presented here with a motive of creating awareness among bioinformaticians about MSA tools that helps in constructing phylogenetic trees.

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Index Terms

Computer Science
Information Sciences

Keywords

Multiple Sequence Alignment Neighbor-joining Upgma Distance Matrix