Do total number of links in main navigation play a role in ranking?
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On one site I work on, I noticed that pages in the upper navigation that have less links in the main navigation vs pages that have more links tend to perform better in organic search.
Has anyone else noticed this?
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I'm a little confused to your questions. Can you explain a little more.
Internal Link structure does have correlation with rankings. I really should say that "smart internal linking" has correlation to rankings. Also, external links (obviously) It may be a situation where some pages are linked to more than others. Have you used any tools (opensiteexplorer.org or WebMasterTools) to see your site's links?
If you can, post a link to your site so we can see it and explain a little more about your questions.