Looks to me as if at least the alignment visualization itself was created with TEXshade (see also LATEX Tools for Life Scientists. TEXshade has a shading mode called 'black' and 'greys' which should do the job.
If that figure is from a publication, I'm assuming it had some graphics editing/formatting/etc performed after the alignment was made, so it is very possible that none of the available graphical alignment software have these colors built in by default.
My bet would be they did a multiple sequence alignment in something like Jalview using a special coloring specification. In Jalview, the colorization profile percentage identity gives a similar looking gradation. The image is then exported into Photoshop, where a simple black & filter is applied, and the image saved. So, with minimal post-processing, the figure will look very similar, if not identical. Hope it helps!