Ribbon plot cannot deal well with 100+ contig genomes

[chriswyatt1]

When your genome is not chromosome level, the script to sort the chromosomes on the plot does not work.

At the moment the script looks at species A, chromosome 1, and checks what is the best (longest) equivalent in species B, then goes on to chromosome 2 and does the same,,, this works for 121 chromosome orders (reasonably well), but not when the genome is in contigs.

We need to edit syntenous_chromosomes.pl to force the contig order in sp2 to be based on the position they are in sp1.