You can make an animation and export a movie in
Poser, in a format for Flash (.swf). This you take directly into Flash, for use.
You would set the background colour in
Poser, to the transparency colour you want in Flash (i.e. black, green).
You would want a colour that is not present in the animation.
Or for a GIF, you can make an animation in
Poser, and export out the movie frames in image format for manipulation, in external programs for processing.
You can assemble a GIF, image with a free program like Beneton (Google "beneton movie gif"). There are others, yes there is Flash, but we like freeware here.
You mention GIF, and also Flash (swf) indirectly by the transparency you are after, the two are separate formats, even though Flash, can output GIF, a GIF is not transparent.
I assume you are going to use
Poser for your animation, so I mention it above, and hence my reference to a movie being output to Flash (swf) files as you want transparency.