Understanding the historical relationship between living organisms has been one of the principal goals of evolutionary research. Phylogeny, i.e., the evolutionary history of a set of organisms, plays a major role in representing and understanding the relationship among various organisms. A phylogenetic tree reconstruction method was developed that detects and reports multiple, topologically distant set of proteins from diverse organisms chosen for the present study. The method is a generalization of the Neighbor-Joining (NJ) method of Nei and Saitou, and affords a more thorough sampling of the solution space by keeping track of multiple partial solutions during its execution. The tree was constructed based on the NJ plot. This report deals a brief account of the various algorithms such as Needleman-Wunsch and distance based methods such as NJ algorithms that have been used to analyze various protein sequences, which perform multiple sequence alignment and construct phylogenetic trees to derive their evolutionary relationship. In the present study, 14 different species starting from fission yeast and nematode to the highest order of chimpanzee and humans were analyzed with as many as eight housekeeping proteins including the tumor suppressor proteins. The results show net divergence of each species from other species. The major findings reveal that humans and chimpanzee are closely related in the proteins like dicer1 and p53, while most other proteins indicate that mouse, chick and humans are closely related in terms of evolution.

Phylogeny, i.e., the evolutionary history of a set of organisms, plays a major role in representing and understanding the relationship among various organisms. Role in representing and understanding the relationship among those organisms. The rapidly growing host of applications of comparative genomics has moved phylogeny to the forefront as an indispensable tool for analyzing and understanding the structure and function of genomes and various genomic regions (Ruths and Nakhleh, 2005).

A brief description of the relevant properties pertaining to our project area, algorithms used (Needleman-Wunsch and UPGMA and Neighbor-Joining (NJ)) and their use in the construction of phylogenetic trees along with the results obtained from the study of the selected protein sequences are discussed in the subsequent sections. The rapidly growing host of applications of comparative genomics has moved phylogeny to the forefront as an indispensable tool for analyzing and understanding the structure and function of genomes and various genomic regions.

Reconstruction of ancestral relationships from the avalanche of contemporary data is extensively used to provide both evolutionary and functional insights into the biological systems. Increase in the available DNA sequence data has increased interest in the phylogenetic analysis of multi-gene families, reprobing into the evolutionary relatedness amongst the species from the lowest to the highest order. Three general classes of phylogenetic reconstruction methods are commonly used for analysis of sequence datasets: parsimony methods (Swofford, 1996), distance based methods (Fitch and Margolish, 1967) and maximum likelihood methods (Felsenstein, 1982; and Felsenstein, 1988). Out of these, the distance-based methods are most often used largely because they are computationally faster and allow a larger number of potential phylogenetic trees to be evaluated.

Phylogenetic Tree, Housekeeping Proteins, Distance Based Methods, Cladogram, Distance matrix, Phylogenetic tree, UPGMA, Needleman Wunsch algorithm, Neighbor Joining algorithm, NJ, Phylogenetic analysis, Biological systems, Operational Taxonomic Units.