I have to find the gene order (synteny) among two organism. The problem is i dont have draft genomes for any. For one organism i have ~17K scaffolds length ranging from (3MB to 500bp) and for another have ~18 super scaffolds (NCBI generated. each size > 13MB bp). I did the blast and tried to visualize in artemis-ACT tool. But it was very clumsy. Thought of circos plot, but i am not sure about it. How do i find the synteny when there are huge number of sequences and are there any better tools for visualization.