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If you are developing this J2EE for an existing organization (client) then, the specific frameworks and products used by the organization is driven by its technology stack. For example, my company uses IBM WebSphere, IBM DB2, Struts framework for building web applications. Recently, a strategic decision was taken to move from WebSphere to Tomcat server. In most cases the architects decide what technology is permissible in that organization.
However, if you are just experimenting, then get hold of a good ide - NetBeans, Eclipse and they come with all the tools you need to run a local application. For example, both NetBeans and Eclipse has support for Struts, Tomcat, WebSphere etc.
Hope I have answered your question.