Antimatter is used to perform most abilities. Unless disabled by abilities, a ship's antimatter pool will regenerate slowly over time. Antimatter pools are primarily found in ships, structures, and Starbases with usable abilities. With the appropriate research, the antimatter regeneration rate can be increased (The Power Core Relic artifact also helps.) When a ship makes a phase jump, it usually loses a hundred points of antimatter, though this penalty can be reduced through research or by finding the Jump Drive Relic.
In terms of tactics, antimatter can be a heavily limiting factor in a battle. After a skirmish has stretched on for a long time, abilities may be less available for use as a ship's antimatter dwindles. This can greatly reduce support ships' usefulness, since many such ships are weak in direct combat. For instance, the Dunov Battlecruiser possesses several useful abilities, but, once low on antimatter, the ship can become a liability instead of a boon--though standard weaponry is not affected by antimatter levels.
Several external factors can affect antimatter. All Starbases gain the Jump Destabilization passive ability, which removes a large amount of antimatter from any enemy ships leaving the gravity well. Neutron Stars also inflict the Jump Destabilization effect, but are able to overpower standard protective measures. Most other stars will also boost antimatter regeneration for ships within the star's gravity well. The Advent tactical structure Temple of Renewal (also known as the Antimatter Recharger, prior to Rebellion) is capable of boosting antimatter regeneration for nearby friendly ships, which can turn the tide in a battle of attrition.