Bioinformatics is the field of science in which biology, computer Science, and information technology combined into a single discipline. Bioinformatics has become an important part of many areas of biology today. It plays a role in the analysis of gene and protein expression and regulation. Bioinformatics software tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. Computers have become an essential component of modern biology, they help to manage the huge and increasing amount of biological data and continue to play an essential role in the discovery of new biological relationships. As there are a lot of Applications based on gel image analyzer such as genotyping, fingerprinting and other application that used in the case of crime scene. It was a must to develop Toolbox to facilitate analyzing the biological data and we start by developing a software tool for analyzing the gel images from biological experiments. The thesis illustrates a new software called EGBIOIMAGE that is designed and developed under windows operating system using C-sharp programming language for analyzing gel Electrophoresis images. It has a very friendly user interface which guide the user from the step of uploading gel image toward getting the molecular weights of unknown bands and generating the Phylogenetic Tree. It provides the user with the ability of processing the gel image using a completely manual processing and automatic processing with the ability of manual correction of lanes and bands “Semi-automatic process” and it is more accurate than comparable software in some respects and the only software that divides the bands into groups and labeled them with numbers in the gel image based on their group by implementing k-means algorithm and these claims are supported with experiments.