A survey of Tools for Phylogenetic analysis using Molecular Sequences

CAP5510

Bioinformatics

Team:
Saurin Desai

Abstract:
The basic idea here is to compare the phylogenies created with various methods available in public domain. The methods considered here are UPGMA, Neighbor join, Maximum Likelihood and Parsimony for Phylogenetics.

Plan of action:
This project is going to try out different phylogenetic methods with different sets of data and compare the results.

Neighbor-joining methods
Phylip package (Felsentein, 1993),
ClustalW and X (Thompson et al., 1994),
Distnj in the Molphy package (Adachi and Hasegawa, 1992)
MEGA

Datasets and Source:
The Anthropology department at the University of Florida has kindly provided me DNA sequence samples for JCV virus. The samples are collected in a different countries of the world and also for various ethnic backgrounds.

Goal:
The purpose is to gather and compare various results from the tools mentioned above. The datasets will be run using the tools mentioned above.

List of papers:
The list in this section will be updated periodically.
Krane, D.E. and Raymer, M.L. Fundamental Concepts of Bioinformatics. (ISBN 0-8053-4633-3) Mount, D. W. Bioinformatics: Sequence and Genome Analysis, (ISBN 0-87969-712-1)
Phylip Program, version 3.62. URL: http://evolution.genetics.washington.edu/phylip/
PhyloDraw Program, version 0.8. URL: http://pearl.cs.pusan.ac.kr/phylodraw/