High-throughput sequencing technology has provided us with a wealth of data. The analysis of these sequenced genomes is not possible without di erent bioinformatics methods and tools. This thesis summarises the tools and analyses that we have provided for understanding the genomes of prokaryotes. We introduce an ortholog clustering algorithm that can be used to nd orthologous genes to help with annotating genomes, as well as nding the evolutionary relationships between them. We then compare the

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... accuracy of this tool with other well-known models and discuss ways for improving the accuracy of the method. We used transposon insertion to study the essentiality of genes in di erent genomes from Enterobacteriaceae family to nd the essential processes in this family as well as in each individual genome. We also compared the set of essential genes in this family with other prokaryotic families to nd genes that are essential in all prokaryotes. In addition, we discuss sources of error and appropriate precautions in order to obtain accurate results from transposon insertion studies. Finally, we present a visualisation method that can be used to facilitate the study of large datasets by making it possible to look at the relationships in a network in a single image. We compare it with other methods and showcase its uniqueness in presenting multi-layer networks.