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(Moderators Note: Original title was "custom template / wordpress functions?")

I'd like to use a modified WordPress theme template and was wondering where I can find a reference for the .PHP functions that can be used within theme templates?

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You can find an extensive function reference on the codex here.
http://codex.wordpress.org/Function_Reference

And there's also the WordPress PHP Doc which can be found here.
http://phpdoc.wordpress.org

Anything in particular you were looking for?

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See the Codex for a reference of all the WP related functions, and the developer section for info about the function that you can use in your template!

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