It's a good idea to have a directory on your website?
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Currently I have a directory on a sub domain but Google apparently sees it as part of my main domain so all outgoing links may be affecting my rankings?
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i would say that it's ok to have outbound links on your site as long as the links are to established trusted sites.
More on the topic on this link including a quote from Matt Cutts on this question . http://lincontex.com/the-missing-link/googles-matt-cutts-vindicates-controversial-theory-behind-lincontex-com/
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