Hierarchical and K-mean clustering, according to their ability to meet the needs and problems of research in several scientific disciplines, are widely used among researchers. Extensive use of clustering in different contexts of health, engineering, social sciences and humanities, lead to growth of knowledge in these sciences. R, SAS and MATLAB software are the most widely used software in the analysis of clustering because of their ability in programming. However, each of this software has particular ability and limitations to clustering. So the familiarity of researcher with clustering method in each of this software allows them to use software which meets their needs for performing hierarchical clustering and K-means.