Home   >   CSC-OpenAccess Library   >    Manuscript Information
Application of New Distance Matrix to Phylogenetic Tree Construction
P.V.Lakshmi, Allam Appa Rao
Pages - 1 - 5     |    Revised - 15-10-2008     |    Published - 15-11-2008
Volume - 2   Issue - 5    |    Publication Date - October 2008  Table of Contents
Phylogeny, Bioinformatics, Distance matrix, Phylogenetic tree, neighbor-joining algorithm, Clustal X
Phylogenies are the main tool for representing the relationship among biological entities. Phylogenetic reconstruction methods attempt to find the evolutionary history of given set of species. This history is usually described by an edgeweighted tree, where edges correspond to different branches of evolution, and the weight of an edge corresponds to the amount of evolutionary change on that particular branch. Phylogenetic tree is constructed based on multiple sequence alignment, but sometimes alignment fails if the data set is large and complex. In this paper a new distance matrix is proposed to reconstruct phylogenetic tree. The pair-wise scores of input sequences were transformed to distance matrix by Feng Doolittle formula before solved by neighbor-joining algorithm. Two data sets were tested with the algorithm: BChE sequences of mammals, BChE sequences of bacteria. We compared the performance and tree of our result with ClustalX and found to be similar.
1 Google Scholar 
2 Academic Journals Database 
3 ScientificCommons 
4 CiteSeerX 
5 iSEEK 
6 Socol@r  
7 ResearchGATE 
8 Libsearch 
9 Bielefeld Academic Search Engine (BASE) 
10 Scribd 
11 WorldCat 
12 SlideShare 
14 PdfSR 
15 Chinese Directory Of Open Access 
ClustalX program. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25:4876-48822.
H. Zhu and J.F. Klemic et al. Analysis of yeast protein kinases using protein chips. Nature Genetics,26(3):283–289, 2000.
M.Y. Galperin and E.V. Koonin. Comparative genome analysis. Methods Biochem. Anal.,43:359–392, 2001.
N. Saitou and M. Nei, “The neighbor-joining method: A new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, Vol. 4, 1987, pp. 406-425.
Partitioned optimization algorithms for multiple sequence alignment. Yixin Chen Yi Pan Ling Chen, Juan Chen.
S.B.Needleman, and C.D.Wunsch, “A General method applicable to the search for similarities in amino acid sequence of two proteins”, Journal of Molecular Biology 48 pp.443- 453,1970.
Studier JA, Keppler KJ: A Note on the Neighbor-Joining Method of Saitou and Nei. Mol Biol Evol 1988, 5(6):729-731.
Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996).Phylogenetic inference. In Molecular Systematics (ed. D.M. Hillis, B.K.Mable, and C. Moritz), pp. 407.514. Sinauer Assoc.,Sunderland, MA.
T. H. Reijmers et al., “Using genetic algorithms for the construction of phylogenetic trees: application to G-protein coupled receptor sequences,” Biosystems, Vol. 49, 1999, pp31- 43.
T. Hodge, M. J. T. V. Cope, “A myosin family tree,”Journal of Cell Science, Vol. 113, 2000, pp.3353-3354.
T. Smith and M. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, pp. 195–197, 1981. Mol.Biol.Evol.,4,406-425(1987).
X. Gu. Maximum-likelihood approach for gene family evolution under functional divergence.Mol. Biol. Evol., 18(4):453–464, 2001.
Mr. P.V.Lakshmi
- India
Mr. Allam Appa Rao
- India

View all special issues >>