Source: http://searchengineland.com/8-tools-google-penalty-recovery-216649
Wondering if your site has been hit by a penalty? These 8 tools will help you assess and fix existing issues on your site.
Recovering from a Google penalty
1. Fetch As Google – This tool will allow you to simulate how Google is crawling URL on your site. It will then give you the option to submit that URL to the index.
2. Screaming Frog Web Crawler – If you think you have been penalized, this tool will help crawl a site and will then find problems such as thin or duplicate content, dead ends, internal redirects and other common issues.
3. Majestic SEO – An especially helpful tool when cleaning up your site’s backlink profile as it allows you to analyze the link profile of your (and your competitors’) sites.
4. Ahrefs – A very effective tool for inbound link analysis and detailed backlink reports. It tells you your site’s overall quality and pinpoint specific problems with individual backlinks that may be flagged as unnatural or spammy.
5. Monitor Backlinks – Since google supposedly ignores any nofollow links, importing your links from Google Webmaster Tools into Monitor Backlinks will allow you to look for your dofollow backlinks and then filter to switch to external to manually verify the backlinks.
6. Copyscape – In case you are suspecting that you are dealing with a content-based penalty from Google, this tool will help you find out whether your content exist elsewhere online.
7. Moz’s Google Algorithm Change History – This tool can be used as a great reference when diagnosing algorithmic issues – a valuable tool in finding out what may have gone wrong with your site when experiencing unexpected decrease in traffic.
8. Google Webmaster Tools – For every site, this tool is a vital(if not the most vital) resource. It will directly notify you if there are any manual penalties Google has imposed for your site. If you see that a manual action has been taken against your site, you’ll know that you need to work to get rid of duplicate content, disavow spammy backlinks, fix broken links, etc.