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The development, implementation and testing for Security of Business to Business and Business to Customer Software Applications System is based on the Central Dogma of Molecular Biology (CDMB), where we derive DNA Cryptographic Keys based on evolutionary models as public-key algorithms are based on mathematical functions rather than on substitution and permutation involving the use of two separate keys, in contrast to symmetric encryption, which uses only one key. When aligning the DNA sequences of the same gene from related species, there will usually be differences between the sequences because of evolution and because of the degeneracy of the genetic. Based on evolutionary models we extract and align the DNA sequences of the same gene from related chosen species with respect to human DNA Sequences. The alignment in the evolutionary system pipeline is realized with ProbCons tool, which is a pair-hidden Markov model-based on progressive alignment algorithm that primarily differs from most typical approaches in its use of maximum expected accuracy. After aligning our extracted DNA Sequences with ProbCons we derive the private/public pair DNA cryptographic keys based on evolutionary models mathematical functions used for Security of Web-based Business Processes Software Applications.