Originally posted by Mystery muppet
No, the Mantu. (Or was it Mentu? I can't separate the two for the life of me...) The Nephilim have been code-named, a lot like the Shivans in Freespace 2. No one knows exactly what they are until it's revealed.
Like LOAF said, the Nephilim are the Star Gods, and the Mantu are something entirely different.
The Nephilim - Star Gods connection is hinted at in game (they show up in Kilrah first, its implied that the Kilrathi are not called 'the unaligned' while the humans are - which probably means a past Kilrathi connection, etc...), and apparently spelled out in the background design docs.
The Mantu, in comparison, are specifically mentioned in the manual, along with the all important information that the Kilrathi lost when they fought the Mantu - which was before the Kilrathi went to war against Confed (the Mantu handily defeated the Kilrathi fleets and then ignored them). The Prophecy was filled with rather grotesque warnings about what would happen should the Kilrathi fail, and if the Mantu were the Star Gods, it is doubtful they would have ignored the Kilrathi.
Just for fun - Shivan/Nephilim comparisons and contrasts
Both have huge black ships with lots of sharp, spiky things on them (although the smaller Nephilim ships are a lot smoother than the smaller Shivan ships).
Both have advanced technology compared to humanity.
Both literally come out of nowhere and launch an offensive.
Nothing is known about the original home, culture, or motivations of either race.
The Allied races in the games have legends regarding cosmic destoyers, and said legends are interpreted to mean the Nephilim and Shivans.
The Nephilim are very vocal while the Shivans are utterly silent.
The Nephilim are a biological life form, while the only current candidate for a Shivan life form appears to be a construct of some sort.
Aside from the Lucifer (basically its shield), Nephilim combat technology appears to be superior in every way, shape, and form to Shivan technology. The Nephilim can open worm holes, while the Shivans are still dependent on devices built by the Ancients to keep unstable subspace nodes open. The only possible exception might be in beam turret technology, as Nephilim anti-cap ship weapons tend to focus on bombers and cap missiles (but since there's currently no way to compare the damage potential of the weapons on each side, even this could be off).
The smaller Nephilim ships (corvettes and fighters) tend to look more Vasudan than Shivan (more rounded, few or no sharp projections, etc...).
The Nephilim spend almost the entire game on the defensive, while the Shivans spend the entire game on the offensive (in all fairness, the Shivans send a much bigger fleet than the Nephilim do).
Note: this is just for fun. Feel free to add, and don't take it too seriously.