What tools you can recommend to visualize the synteny/comparative genome of 2-4 species/cultivars specifically structural variation among species?
Similar to Gale et al 1998 check image.
Thanks
Hi,
Try any of the following:
1. ACT - http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
2. BRIG - http://brig.sourceforge.net/
3. circos - http://circos.ca/
Best regards,
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Diran
For circular comparison profiles Circos is the best option. A little bit tricky to use (steep learning curve), but it provides great results. Have a look on the Circos Images section on the website: http://circos.ca/images/
The authors provide very interesting tutorials, and the software is very well documented.
For linear comparison profiles, ACT is perfect, and very easy to use. It's just a matter of blasting the genomes (pairwise) and using the Blast output in tabular format as the comparison file ('crunch' file).
Well .. circos looks glossy, but not all chromosomes are circular. You can try http://eh-demo.ncsa.uiuc.edu/ for better comparative overview.
Here are a bench of tools, I used many of them but all.
https://omictools.com/comparative-genome-visualization-category
Best.
Loub
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