Abstract
One of the significant steps in the analysis of phylogenetic relationships between species is the DNA sequence comparison. In this paper, a fast method for comparing DNA sequences was introduced based on the frequencies of the codons it contains. The frequencies of codons are calculated in a way where the similarity of DNA sequences can be avoided. The method is tested for 15 species in both short and long DNA sequence. A software was implemented using wxpython that uses this method and tests it. The results were compared manually with the data in NCBI, and it was found that our method works well, thus proving its benefit. Finally, to make this method available for specialists, a software is uploaded using this method to cloud depends on cloud computing platform, "Google App Engine".