4 answers
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.
Andreas
Hopefully you got a solution using our program Jalview. Another way to do this would be to use ALSCRIPT. It is not point and click, but allows a lot of options for grey scale shading.
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!
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Do you also want to display the secondary structure and dendrogram, or is your main goal black/white/grey shading?
Sorry, I meant that only to visualize the sequence alignment. Do you have any suggestions?
Might be able to research options if you supply the source of the figure - is it from some article?
Are you looking to do the alignment and coloring in the same software, or you open to using photoshop?
I think it would be better to color it in the sequence visualization software.
I see, that pictures are partly from bioedit. I use bioedit, or MEGA for such kind of figures.
Thanks! I think Bioedit cannot provide such a figure (black/grey/white). Would you please tell me how to do it with Bioedit?
I used this button http://rghost.net/49399357/image.png
Thanks so much! I think there is a small problem about it. This button allows coloring all columns. In the figue shown above, not all columns are colored blakc or grey. Besides, not all residues in the same column are colored. I was wondering if it is possible to to it. Thanks a lot.