Missile and Cannon setup?

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    Is there any particular way to set up Missiles and Cannons to get the most DPS from them?
     
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    Keep adding lots of them. That's about it. Also, make sure you use the slave system.
     
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    DPS is determined by the size of the weapon, as long as you don't go over 100% slave or effect every block will add damage, 5 DPS per block. Any slave that reduces fire rate increases damage (pulse and damage beam), and any slave that increases fire rate reduces damage (cannon). Now when you start adding effects you have to consider how they affect that damage. Ion will add more shield damage but make you deal less against every block. Pierce lowers shield damage but can deal a lot more hull and system damage.
     
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    Additionally you need to remember that the DPS is not affected by the Slave System only the "per shot" damage is affected.
    So a rapid firing weapon does less damage per shot, but pumps out more shots in the same time, while a slow firing weapon will do more powerful shots but fewer in the same time.