Gene and species limit

[IzenR]

I need to plot a locus with around 20 genes across 13 species. Does anyone know the upper limit of the number of genes/species that works with the clinker? I also need to hilight a block of deleted genes in a subset of the genomes. Would clinker be able to handle it?

[gamcil]

That should not be a problem. There is no hard limit, just that the alignment method clinker uses is not going to be efficient for larger regions (e.g. whole genomic contigs). You should be able to see the block of deleted genes in the clinker output (since there will be no genes in that region), but there is no built in method to highlight it. You would have to do that in external software.