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Currently I need to revamp a university website. The problem is some of the links actually go to different microsites (within the same domain) that have different layout. The only way to link back to main site is by clicking the logo which will bring to homepage.

enter image description here

Above is the sample of the current navigation. Those with purple underline will open a new tab of microsite.

How should I display them better? For faculties, I am planning to separate them from the main navigation, like below:

enter image description here

This way, it doesn't disturb the whole experience. However, I still find it weird that admission linked to a microsite with different layout. Is there any way to avoid this? Or is it actually okay to have some links in top menu that open up a new tab?

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It is absolutely okay to have some links in top menu that open up a new tab. I work for an eCommerce websites and different application symobols take my users to their respective landing pages.

make sure you open them in a different tab so that way they do not have to go back to the mail site. They can just close it.

The best way is to maintain the visual consistency and build one website with different landing pages but if your priority is not to redesign those micro sites, just open it in a different tab.enter image description here

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You can use a mega menu to display the homepage of those websites you are talking, and open them in a different tab of course. This way users will be at least advised.

Here is an example of how it can be managed Example of mega menu for a french company

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