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When I browse the site (chrome or firefox most of the time) a list of questions appears on the right side.

It's divided in two categories: linked and related. The number of questions in the Linked part is far less than in Related (there is often only one question linked, but sometimes there are more). Also, the questions in Linked often appear in Related.

What are the differences between these two categories?

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Linked questions are ones where there is an actual link somewhere in the question, answer, or comments to or from another question or answer somewhere on this site.

For example, let's look at this question: Are we sure about the regeneration order of the Doctor?.

There are two linked questions:

The first of the two linked questions is referenced in this answer to our example question, in the form of a link in the second list item.

The second linked question isn't referenced in our example question, or any of its answers. However, it is shown as linked because this answer on the linked question contains a link to our example question in the last paragraph.

Related questions, on the other hand, are automatically selected based upon a vocabulary matching algorithm.

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    Wow, I find the algorithm to find the linked questions even more magical than the one for related questions... Thanks, I'm not a native speaker and I thought "linked" was just a synonym of related, didn't think of taking it first degree. – Kalissar Nov 25 '13 at 16:56

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