Computational Analysis of Distance and Character based Phylogenetic Tree for Capsid Proteins of Human Herpes VirusVipan Kumar Sohpal1*, Apurba Dey2 and Amarpal Singh3
- *Corresponding Author:
- Vipan Kumar Sohpal
Department of Chemical & Biotechnology
Beant College of Engineering & Technology
Gurdaspur Punjab, India
E-mail: [email protected]
Received Date: March 23, 2013; Accepted Date: March 27, 2013; Published Date: April 03, 2013
Citation: Sohpal VK, Dey A, Singh A (2013) Computational Analysis of Distance and Character based Phylogenetic Tree for Capsid Proteins of Human Herpes Virus. J Data Mining Genomics Proteomics 4:128. doi: 10.4172/2153-0602.1000128
Copyright: © 2013 Sohpal VK, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Molecular phylogenetic is a fundamental aspect of evolutionary analysis and depends on distance & character based methods. In this paper, we compare the viral capsid proteins of HHV to analyze the relationship among proteins using substitution models, phylogenetic model with exhaustive search and ME techniques. The effect of Poisson correction with shape parameter on NJ and UPGMA trees also analyze. We show by extensive computer simulation that phylogenetic tree is the reflection of substitution distance. The effect of max-mini branch & bound method and minimini heuristic model and log likelihood associated with character based tree also discussed. We applied ML and MP for perfectly analysis of proteins relationship. We conclude that substitution models, shape parameter, search level and SBL have a critical role to reconstruct phylogenetic tree. Molecular clock study shows that χ2 value is higher in closely as compare distant related proteins.