How to make a Multiple-sequence alignment representation figure like this

Question

[xyc_liang]

Use red bars and black bars represent the non-synonymous and synonymous mutations in the alignment. Blanks indicate deletion. Is there any program or script could make it?

just like fig.1 in this paper http://www.pnas.org/content/106/23/9519.long

[xyc_liang]

[GenoMax]

Paper describes using ClustalX and GeneDoc which are both free programs. Many figures are post-processed using an image editor so you may not be able to get the exact result you see in a paper from just the programs mentioned.

[xyc_liang]

I get it. I just like the style. Another paper published by their group mentioned that the representation was generated by a home-made PERL script. So I wonder is there anyone has this type of program or script?

Answer 1

[EVR]

Use software ClustalX to generate the exact figure like in paper

[xyc_liang]

The alignment was performed by ClustalX, but the schematic representation of sequence alignment was generated by some other programs or scripts.