You cannot use EJB on Tomcat (unless you add OpenEJB). If your WebSphere deployment uses EJBs, you will have to remove them to deploy to Tomcat.
If you use any Java EE functions outside the servlet / JSP engine and the JNDI naming service, you will have to exclude them from your application.
Tomcat accepts WAR packets. If you pack the application in an EAR in WebSphere, you will have to change it to a WAR for Tomcat.
Both use JNDI for data sources. There may be some disagreement in naming conventions, but if you adhere to the standard, they should be portable.
If you use any specific WebSphere code in your application, you will have to remove it to deploy to Tomcat.
If your application is servlets, JSPs, and JDBCs, you can deploy them without problems.
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