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Check out http://www.tomcatexpert.com/blog/2010/07/07/how-migrate-jee-applications-tomcat for a nice discussion on how to migrate from jee to a light-weight alternative like Tomcat - with Atomikos for JTA if needed.

Of course, you can also use Jetty from Webtide (which has Atomikos pre-integrated into the Hightide edition)...

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