Transphasic torpedoes are powerful weapons from the future Federation.
Except for the obvious fact that they do a very good job of destroying Borg Cubes, these weapons remain an almost complete mystery. The name suggests that they defeat the frequency-specific shielding of Borg vessels by changing their own frequency or phase alignment.
Transphasic torpedoes appear only in "Endgame", the final episode of Star Trek: Voyager. As yet, there is no indication that "modern" Starfleet was able to reproduce these futuristic weapons. As they were developed within the lifetime of Kathryn Janeway, the Federation should be capable of inventing them within a few decades.
Transphasic torpedoes work by delivering a subspace compression pulse existing in an asymetric superposition of phase states. If one subcomponent of the pulse is blocked by shielding, enough others will still succeed in penetrating to the target to ensure that the majority of the pulse is still delivered. Each torpedo's transphasic configuration is different, randomly generated by a dissonant feedback effect, so there is no way for the Borg to predict the configuration of its phase states in order to shield against them.
The Enterprise-E was initially equipped with them in 2380, however by late Febuary 2381, during the Borg Invasion of 2381, Starfleet gave the schematics to the transphasic torpedoes to all the ships in the fleet after the Borg sent 7,461 ships through a subspace tunnel in the Azure Nebula. The Borg eventually adapted to the torpedoes.