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Here is a great tool I've been using that can determine if you have bad links pointing to your site.
This tool was recommended by SEOMOZ.
If unhealthy links are found, you can simply create a file ready to upload to Googles dissavol tool.
You can find it here. http://www.linkdetox.com/
How does it determine what a bad link is?
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the tool analyzes all your backlinks up to 60,000 and gathers 93 metrics that it applies automated best-practice SEO rules against. That means after processing all that data, you get recommendations about which links are toxic and should be removed ASAP, as well as which links are suspicious and need further investigation.
The tool detects all kinds of issues, like from a sharp drop in link growth for the linking site (negative link velocity) to typical link network patterns like same domain owners, similar IPs or DNS, and a lot more.