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Tomkins, a half back and the younger brother of first team player Joel, has signed a new deal until the end of 2010, with an option of a further year.
Flanagan, a loose forward or stand off joined Wigan from Bradford in January 2007, and has signed a one year extension to his current deal which will take him until the end of 2009.
Speaking about the contract extensions Wigan Chairman and Owner Ian Lenagan said: