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I have Flash 5 but haven't used it much. As far as I know the only way to do it with Flash would be to import individual pictures/frames in, but that used to make the flash files way, way too big for most purposes. I don't remember if I could control the frame speed to make it go fast enough either.
We do want to be able to show these animations on a web page too, so the software would have to be able to be saved in a file format that would allow that.
Failing that, there is software to compile frames into Mpeg movies. That should do the trick. Most video software allows the compilation of frames, but I think 'cmpeg' which is an old freeware application may be better for you.
I still trying to find information about cmpeg.
Get virtualdub, open it and from the top go to file>open video file ... from the file types drop down box select image sequence. Select the first image in your image sequence. Thi will load all the images into virtualdub and set the frame size to whatever the images are.
Go to video and make sure "full processing mode" is selected. Also if you need to adjust the framerate you can select framerate to change it. Under compression make sure "uncompressed" is selected.
Go to file>save as avi ... save it. You use this file as source in other applications and can pretty much go anywhere with it. It's not suitable for anything else because its going to be huge in file size.
Being that you want to put this on the web I'd suggest loading it into Microsofts Media Encoder and exporting it as WMV which will give you a very compressed but high quality video.