Entering edit mode
11.0 years ago
jth
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190
Dear All,
I am looking for a software (free/open-source preferable) that can produce publication quality alignment images. An unfortunate requirement is that the software should be cross-platform as it will be used in a highly heterogeneous environment. Do you have any suggestions in this matter?
Thanks!
Could you give an example of a publication quality alignment image? The ones I've seen differ _a lot_ in quality, and I suspect that in the nicer ones there's been some manual editing involved.
It sounds a lot like the job of IGV and Tablet, although the meaning of publication quality alignment image really depends...
This is a slightly good instance i guess: http://www.nature.com/nature/journal/v392/n6671/images/392097ab.tif.2.gif It has been colored for particular reason in particular positions (it may be just to show sequence similarity, of course), It has well represented helices or other secondary structures, and it is easy to follow the alignment in the figure.
That particular alignment actually looks like it's been done manually, especially since it's from a '98 article. Also, I believe the residues are coloured by physical properties. E.g. if all residues on the same position are non-polar. There's quite a few different kind of markups, each having its own merit.
If you want that kind of alignment, though, I think your best best if to look into IGV or Tablet, as someone mentioned. Another (free) option would be Jalview, however that doesn't add in secondary structure to the actual alignment, so you would have to do that yourself. And it's run in Java, so it's fit for a cross-platform environment.