I need to draw some graphs like above to show the conserved gene order between different strains. So do you know some software can draw such a graph automaticly. Because I have a long list to draw. And I have the genbank/ptt/gff format file, I hope that software can read one of those format.
Thank you very much!
The AnnotationSketch tool (part of the GenomeTools library) can read data in GFF3 format and generate PNG graphics. Color coding is highly configurable, but I the legend wouldn't be possible without some post-processing with something like Photoshop or Gimp.
Since you have gff files already, I would recommend GBrowse_syn, though I have to warn that if you are not familiar with GBrowse already then configuring GBrowse_syn may not be worth the effort just to create some graphs (you need a database of alignments, not just annotations, for this to work). SynView is another synteny viewer that uses GBrowse, but with a completely different design. SynView ships with some test data and I know the author still works on related projects, so he will likely be helpful. If you are starting from scratch, you could just use Mauve, which will create a graph showing the synteny between the genomes.
Try this. It has a friendly user interface and is very easy to use. Scaleable to a large number of genomes. Also does labels. http://sourceforge.net/projects/easyfig/
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