Do nofollow links affect link profile?
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I've read that it's good to keep a natural link profile. Some naked links, some links going to our company name, some with anchor text, etc.
Do nofollow links affect this link profile, or is it only followed links that are taken into account?
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I can't agree more with William Lau.
When I build links I always do it naturally. If I find a website that is the perfect fit for my campaign then I am going to attempt to get the link regardless of whether it is follow or no-follow. This is natural link building.
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You should allow Page Rank to flow naturally. If your home page link to contact us page does not have nofollow that will allow contact us page to flow some PR back to the home page. If you hit a link on home page with nofollow to the other page then the other page not only can't flow the PR back, but also the remaining page rank will not be given to the links which are not nofollowed.
I think Matt Cutts best explains it. If you see paragraph 8 of this page http://www.mattcutts.com/blog/pagerank-sculpting/ or better still the whole article it should clarify things for you.:)
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All is taken into account. But don't go out of your way to get like 20% this 20% that and 20% of this. Do it naturally and you will have nothing to worry about.
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