How to use this tool.

The only output of this tool is an image. Below we have analyzed the HIV-1 GAG subtype reference alignment.

Now an error is introduced into this alignment - one sequence is out of alignment by 1 amino acid. It is located in the middle of the alignment, and starts to go off in the center. It looks like this using Pixel's default settings:

If you look very closely, you can see a little wiggle, but it isn't very clear. However, setting the scale to 2 we get this:

Which clearly shows a problem. If the error is greater, out of alignment by 4 amino acids instead of one, the image you get is this:

So a misalignment of this size is clearly visible even with the default scale setting of 1 pixel.