I suggest using torpedoes when dealing with the capitals ships. They can deal a large amount of damage and the splash damage from the explosion can destroy and fighters nearby. Equiping one of your fighters or your mothership with a radar might be useful because torpedoes take a long time to fire.
Also the turrets on the alien frigate fire lasers, so a decent laser shield would increase the survivability of your mothership.
And major caliber guns are very helpful whenever you have to deal with captial ships. While the FTU warehouse is a great place to look for these guns, it is not needed. Smuggler bases often sell a few, I suggest looking there first because you will already be fighting pirates for exp anyway.
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