A command sequencer was a component of a starship's computer core involved in systems control.
In 2372, Quark's cousin Gaila finally delivered on a ten-year promise to buy Quark a ship. During its first flight to Earth, the command sequencer of the Quark's Treasure was disabled, causing the ship's warp factor to increase steadily to the point of structural failure. As Rom had checked the systems prior to departure, the only conclusion was that the sequencer had been deliberately designed to fail. (DS9: "Little Green Men")
In 2375, Ru'afo ordered the command sequencer of a transporter aboard the Federation holoship to be rerouted through the auxiliary processor. This allowed the transporter, which had been previously locked and secured, to beam him over to the Son'a collector and his crew to return to their vessel. (Star Trek: Insurrection)
In 2376, Seven of Nine took it upon herself to improve the efficiency of USS Voyager's computer core, by enhancing the command sequencers with Borg algorithms. This caused a number of minor malfunctions throughout the ship. (VOY: "One Small Step")