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My website http://compare.buyhatke.com got hit by the recent algorithmic updates. What I could find out as of now is that I have 3-4 services hosted on different subdomains and we keep a constant navigation bar at the top for all our subdomains so that a user can switch easily between services.

Now the problem is the services are not completely related to each other and due to lots of pages on our websites. The count of backlinks as shown in Google Webmaster Tools has also increased to 109,857,360 which is very large.

So can the backlinks be the culprit given that they belong to different subdomains, and Google might consider them as spammy links, while in reality they are just to simplify navigation, and to keep displaying the top products from each service in the navigation bar?

screenshot

Should I remove the backlinks by using Disavow tool?

Should I use a nofollow tag in all the URLs of my navigation?

What would be the best way to clean up this?

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    Stack Exchange operates just fine without nofollows. It'd be helpful to explain why you think you got hit.
    – Simon Hayter
    May 24, 2014 at 8:52
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    Would also be helpful to know what "hit" means in some way. Maybe just for a certain word?
    – nathangiesbrecht
    May 24, 2014 at 15:09
  • I don't know if any search engine actually does it, but if you mark the navbar with HTML5 <nav>, then search engines would potentially be able to more intelligently deal with the internal cross linking when calculating the ranking.
    – Lie Ryan
    May 24, 2014 at 15:34

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It sounds like you need nofollow in your links. Here is a Google page on the subject:

https://support.google.com/webmasters/answer/96569?hl=en

You may need to modify the links something like this example.

<a href="signin.php" rel="nofollow">sign in</a>
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