[Re-posting because moderator mistakenly assumed it contained a commercial link; it doesn't.]
The most useful I've found is GEDmatch (http://gedmatch.com/
), which can compare DNA cross-company, i.e. FTDNA and 23andMe. It also has tools for comparing GEDCOM files and triangulating your matches, which might help figure out how you're related.
Then there are a variety of projects by both academics and hobbyists to determine the ethnicity of your ancestors more finely-grained than any company currently offers. One academic one, and relative newcomer, is Interpretome from Stanford University (http://esquilax.stanford.edu/
). The most extensive one is called the Dodecad Ancestry Project (http://dodecad.blogspot.com/
), which normally requires four grandparents from the same Eurasian ethnic group. However, he's recently released tools you can use to do the same analysis yourself.
If you are interested in the health aspects of your DNA, you can use Promethease (http://snpedia.com/index.php/Promethease
) to explore that.
That's only scratching the surface of tools available now, and it's an active area of research and development. Here's a whole list of third party tools (http://www.23andyou.com/3rdparty
), which although intended for 23andMe customers, work just as well for data from FTDNA.
[Note to moderators: The last link is NOT a commercial entity. The name of the website, 23andYou, is a play on words about the commercial entity, 23andMe–notice the difference? Please verify your assumptions about links before removing posts, simply by visiting the link in question. The bottom of every page on that website clearly states "Not affiliated with 23andMe." The About page (http://www.23andyou.com/about
), makes it even more explicit it isn't a commercial entity:
"This site is not affiliated with 23andMe.com in any way.
This site was put together by a 23andMe member for the benefit of other 23andMe members. This information on this site was culled from several sources, predominantly from posts on the 23andMe Community Forums. Many thanks go to those who contribute to those forums."]