AutoStakkert!2 (often referred to as AS!2) is free, though a donation is welcome. This is now the preferred option by the top planetary imagers for aligning and stacking the images. Further processing is done in Registax using the wavelets option and then something like Photoshop or Elements 11 which is what I use.
When you open AS!2 you are presented with a split screen with the settings on the left and a box where your image of the AVI will appear on the right. Click on 1) Open and browse through to select you AVI or SER file.
For planets like Jupiter the boxes should be ticked as follow:
Planet, Dynamic Background, Gradient, Autosize (quality based), TIF or PNG (doesn't matter which), Normalise stack at 90%, HQ refine, Drizzle off. And leave Noise Robust set at 2. The number of frames to stack or the frame percentage can be set after the analysis, but 50% is a good value to use if the quality of the video is reasonable.
Now look at your image and the settings there. You can either use a the Single or Multiple alignment points option. If you choose Single then you should draw a box around the image. Damien Peach recommends the Multiple AP option. For this you need to select your AP size - this refers to the alignment point box size and if you click on your image you will see the size of the box. You can then cover the image with these boxes.
However, a far simpler, quicker and more efficient method is to use the Auto AP method and click on that. This will do it for you, though you may have to adjust both the minimum brightness level and the size of the alignment box to get adequate coverage. It is very good for picking up the Moons of Jupiter which you may not otherwise see! If you choose too low a brightness level then the program will pick up extraneous points which are simply noise.
Once this is done click on 2) Analyse and wait. The program will then show you a Quality graph with a horizontal line indicating the 50% level and another variable one following the individual images indicating how these have changed. I think the theory is that on this basis you determine the % of frames to use for stacking, but I have never found any particular correlation between the graph quality and the end result and Damien Peach seemed to agree with this. He suggests 50% be used and that seems to work for most avis's.
All you have to do now is click on 3) Stack and wait. This is the longest process and how long will depend on your computer, the number of frames in the avi, the number of alignment points and the % frames selected. And the end result will be a TIF or PNG file ready to input into Registax. But when I have done several avi's I always clear the AP points, select another avi, redo the APs and Analyse and Stack as before.
With the Moon the settings are except that when you open a video you should select Surface instead of Planet for the Image Stabilisation. This will give you an image stabilisation box in the centre of the image. Click on the x and press ALT+9 to enlarge this box. Now click on 2) Analyse and wait. You will then get a larger red box covering most of the image, depending on how much it drifted during the video. Now click on the Place APs in grid and it should cover the whole of the image in the red box. If the image is too dark you may need to adjust the brightness level, clear and try again. Now 3) Stack and wait. The end result will be a TIF or PNG file ready for waveletting in Registax 6.