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Originally Posted by drkellogs
I have a dilemma, I am building a website that needs to be separated into two separate sites run by two separate CMS as well. (A modified wordpress theme optimized for SEO)
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From a functional standpoint, you've just described subdomains. Especially if your definition of success includes a lot of visitors. It's possible to configure two different CMS or other off the shelf systems to work on a single domain against different folders ( IIS does this by default), but only subdomains would allow them to be hosted on different machines, natively, for load balancing.
Duplicate content has to do with content being duplicated. This seemingly is punished across different sites, but more or less ignored within a site. For reasons that are pretty obvious if you think about them much. It has nothing to do with graphic design.
Subdomains used to be counted as wholly distinct sites. A few bad apples spoiled the whole batch. Bob.wordpress.com is different than alice.wordpress.com, but none of us are WordPress.
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