You will need a Vertex Standard-compatible programming cable (often uses a 3.5mm jack or a specialized multipin connector depending on your specific VX-3000 version).
This guide covers everything you need to know about acquiring, installing, and using the programming software for the Yaesu VX-3000 safely and legally. Understanding the Yaesu VX-3000 Software Requirements yaesu+vx3000+software+free
There is for the VX-3000. However, the amateur radio and commercial radio communities have developed two main free alternatives: You will need a Vertex Standard-compatible programming cable