Yes, it's one of two BOTF2 games in the works. The other (and the original) BOTF2 project is New Beginnings. Star Trek: Supremacy is in its early development stages. You can (hopefully) expect a preliminary release in 2007 with most of the features implemented, but with automated combat only. There will be a second and final release about a year later with 3D tactical combat. There's more information scattered throughout the two Supremacy forums.
This and other questions are answered in the Supremacy
FAQ.