Yep, there are actually a lot of different options at your disposal. A lot of information like this is in the mini-guide, but basically:
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The best defense is preventative. Putting tractor beams around key wormholes is kind of a must. Putting turrets with the tractor beams tends to work quite well. Bear in mind that a few ship types, like Raiders, are immune to tractor beams.
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Ships that are in attack-move mode (hold down the Alt key and then right click, and the border of the ship will turn yellow in far zoom) are also great at defending wormholes, since they can pursue enemy ships that break through. Ships that are in attack-move mode will automatically pursue any enemies that come within their range.
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If you have either Spiders or Infiltrators (two of the 25 “bonus” ship types), those both do engine damage against enemy ships. So if you place them as defenders of a wormhole, they will often disable the engines of enemy ships that come in, preventing them from getting very far or stopping them all together. This only works when you have these units, though, which you won’t in many games.
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To prevent waves from coming into your resource-heavy planets (most especially your home planet), a big focus early on should be to destroy the warp gates at planets adjacent to yours. That will prevent them from warping in at all.
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You are always going to have ships warping in to some of your planets, and managing your defense vs your offense is one of the strategic challenges here. It takes some practice to balance it out, but basically try to leave as few “hostile” wormholes open as possible – or at least get rid of the warp gates near them. Don’t try to get rid of all the warp gates, since that makes the AI Progress go up too much, but get rid of the ones that threaten your most valuable planets if you can.
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If you are having trouble with lots of the little special forces ships just wandering into your planets, a couple of tractor beams pair with turrets will generally handle it. But you may also want to go and destroy the Special Forces Command Posts (use Cruisers for this) on planets through which the most special forces guys are routing.
By combining careful scouting with precision strikes, and defensive ships where need be, you can exert a great control over your environment. There will always be ships on some of your planets, but to a certain extent you can choose which ones. There are a ton of strategies open to you, actually, but it all depends on how aggressive or defensive you want to be, how open you are to heavily attacking the enemy early at the expense of having more of their ships on your planets, etc.
In version 1.004, which is coming out tonight (if you have Impulse you can manually install it, I’m pretty sure, but the update will be officially coming out through Impulse in 1-2 days), there is also a new option called “Free Roaming Defender.” You will be able to put your ships into that mode by holding V and right-clicking, and they will get a hot pink border in far zoom. While in that mode, they will actively pursue and destroy any enemy ships on the current planet, which makes planetary defense a lot simpler (this was a great suggestion by a player).
Let me know if you have any more questions (I’ll post here when 1.004 is out, in case you want that tonight)!