Google Webmaster Tools added a new feature: a complete of the links that point to your site and a list of your internal links. Google's link operator shows only some of the backlinks. Now, because Google trusts you (you validated the site, so you have access to it), you can see the number of backlinks for each page of your site and a list of backlinks.
The interface is pretty difficult to use, especially for large sites, so it's a good idea to download the data and analyze it Excel or other spreadsheet application.
Google's blog says there are some limitations: "We do limit the amount of data you can download for each type of link (for instance, you can currently download up to one million external links). Google knows about more links than the total we show, but the overall fraction of links we show is much, much larger than the link: command currently offers."
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