The old school (and inefficient) way is to create an ANI (with anibuilder)
The better way is to have the single frames in DDS format, and animate it with an EFF file.
Fromt the WIKI:
Animated Textures
Freespace 2 SCP also supports two kinds of animated file format. The first is the standard .ANI extension as used by Freespace Retail, you can convert these using the AniBuilder program from the Descent Tools package. The Second format is the new .eff file. This allows multiple single images to be chained together into an animated texture. All .EFF image files must be in the same format, but can be in any format Freespace SCP supports, and must have an underscore and their Frame number added onto their name as a 4-digit number starting at 0000, for example RunningLights_0000.DDS, RunningLights_0001.DDS etc. Now simply create a new text file for your animated texture with the same Base name as your texture and a .EFF extension (in this case, RunningLights.EFF) and simply enter the following text.
$Type: XXX - Defines the type of file being used, can be DDS, TGA, PCX or others
$Frames: XX - Defines the number of Frames in the total (looping) animation.
$FPS: XX - The Frame Per Second speed of the animation.