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With Yahoo closing Site Explorer today what are the best free tools to track back links to websites?
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Well I'll start noncommittally by saying there are pros and cons to each and every tool. And that each and every tool is going to give you a different answer. I think the important thing to do is to pick to be consistent in the way you are comparing sites. That is, don't compare inbound links to siteA found using tool1 with inbound links to siteA using tool2. Compare siteA and siteB inbound links using the same tool for consistency.
That said, iPullRank posted a blog Eulogy for Yahoo Site Explorer at SEOMoz on the same day you asked your question. Eight alternatives were listed, four of which are free, including the good-old link: command. Try them out and see what you think.
http://www.seomoz.org/blog/yahoo-sunsets-site-explorer-a-eulogy
To save time, here is the list of tools.
Open Site Explorer
MajesticSEO
Link Diagnosis
Google Webmaster Tools
Bing Webmaster Central
Blekko (search [domain] /SEO)
SEO Spyglass
RavenTools Research Central
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