I have never gotten an authorative answer to this question, but I'm posting my thoughts. I've just acquired another ".edu" link to one of my sites. However, it contains a "~" in the URL. If you're not aware, by convention, a "~" prefix on a directory references a Unix home directory web site. These are typically used by students on a shared Unix machine. However, I have also seen quite a few university professors post valuable academic information on such a web site.

Now, it is widely believed that a ".edu" link is worth quite a bit in terms of "link juice." They are prized among search engine marketers — more so than many of the best ".com's." This is because, as most search engine marketers posit, it is much more difficult to socially engineer the acquisition of a ".edu" link; and it is, therefore, a substantial vote from an accredited institution that probably does not stand to benefit in any way from the said link. Search engines love them, in other words. A "~," however, adds another complexity, as it could be a student with a homepage extolling the virtues of Pokemon, or a professor with groundbreaking research recommending a book on particle physics. It's hard to tell.

Therefore, my hunch is that the link's value is deprecated to perphaps the level of a typical non-".edu" link. This is because a home directory site is not under the auspices of the university — at least sometimes. Interestingly, Yahoo! has the said link up high in the list of inbound links, and Yahoo! has the nice feature of collating the links in order of importance. It must be worth something. But I won't get my hopes up. Yahoo also enumerates some "nofollow" links at the top of the list of backlinks as well.

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