As more chloroplast genomes are sequenced their comparative analysis helps to identify conservedness between genomes and provide evidence on the evolutionary history of organisms. In order to increase the significance of similarity search, we defined three new parameters; Cumulative Sum of Homologs (CSH), Actual Proportion of Homologs (APH) and Homology Impact (HI) for post BLAST analysis. These parameters can also be used in other similarity search tools and are useful to identify unbiased conservation between genomes. Moreover, our work demonstrates use of missing data in phylogenetic...