The Colonial Viper is not a war craft in the same way a Colonial Viper is. The Raptor is more a reconnaisance and transportation craft when the job is too small for the Battlestar Galactica to do it. It can be used to transport crew members from one ship to another. When President Laura Roslin needs to be transported from Colonial One, her craft to the Battlestar Galactica, she is taken across in a Colonial Raptor.
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