Can I use IIS as the Web Application Server? I don't know much about Tomcat.
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No. FME Server's web applications are java based. A java web application server is required. IIS is not a java web application server.
IIS may be used in conjunction with a java web application server, for example:
https://knowledge.safe.com/articles/632/using-iis-and-arr-as-a-reverse-proxy.html