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Should I nofollow the main navigation on certain pages?
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We have several large Ecommerce sites with hundreds of links on each page. I have been trying to think of ways to focus our internal linking to increase certain pages relevancy. My thought was to put nofollow in the main navigation (since there are hundreds of links there controlled by dropdowns) and only follow the links on each page for the products we are selling and promoting (15-20 links). I would still be using a sitemap that includes the links. Is this a terrible idea?
if a link is nofollowed in the main navigation does that still count as the one mention for google if it points to the same page that a normal link points too that is in the content of the page?
since all of the main navigation is the same on every page of the website would it be good to only put nofollow on the subpages/subsections and leave the home page navigation alone (that would allow the spiders to crawl all of those links on the home page but not crawl those same links on the subsections where I could then focus the linking).
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I dont see any reason to put or not the follow links in your navigation, unless you want to focus on a certain page for more relevancy, or focusing a certain page for ranking.
If you want to remove your follow links on your navigation be sure you specified your inner pages in your Sitemap.xml, so Google bots can still track your pages.
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Referred to the "long dropdown menú", I suggest to copy a practice I see more and more: to use the mega dropdown just in the home page and disable in the internal pages (maybe creating a sub navigational category menu in the categories' hubs).
I am sorry I have not here with me the link, but that is also suggested by Google in one of their webmaster help answers.
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I am not a big fan of internal link nofollows and find the whole thing more or less pointles and it's better to let Google crawl through your site freely. Site architecture /structure is crucial. One thing we did recently was remove links which lead to same pages and trimmed our link count down by 30%. Another feature we've introduced was a featured box which contained products which we knew needed some internal link love. Typically ecommerce sites have popular products by no way to specify which product pages to feature manually (or at least in a controlled way).
Are you using faceted navigation at all?
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First off, I'd just say that internal navigation controls tend to have only a small impact. That's not to say it's not worth doing, just that you shouldn't expect a massive ROI unless your nav structure is truly horrible

That said, nofollow might not be the best choice - here's why: http://www.seomoz.org/blog/google-says-yes-you-can-still-sculpt-pagerank-no-you-cant-do-it-with-nofollow. You might also want to read - http://www.seomoz.org/blog/an-illustrated-guide-to-matt-cutts-comments-on-crawling-indexation
There are some potential other ways to do this, though:
http://www.seomoz.org/blog/link-consolidation-the-new-pagerank-sculpting
http://www.seomoz.org/blog/whiteboard-friday-faceted-navigation
Basically, my suggestion would be to think about how you could implement some form of consolidation or possibly use less navigation by default (maybe only enable the long drop downs if a user is logged in, or only show them on the specific category pages).
Let me know if you've got follow-ups after checking these out. I'm happy to help further.
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