jcvi.compara.reconstruct zipbed

[Wongolini]

Hello again!

The readme is a pretty limited and I've just been exploring all the programs involved in synteny. I've been trying to figure out what each tool is doing from a combination of reading the code and your published papers. In my case, I have 2200 e. coli genomes, which are obviously much simpler than plant genomes.

I have a couple questions. If I run 2200x2200/2 comparisons, are there any scripts you already have that could dynamically chain together the synteny between all these genomes? When I see the plots you're showing I know it can do this visually, but what is there a single associated file that actually shows these connections, or is it only a visualization that is made from reading all the anchor files? Which script would it be? And then from this, can it construct ancestral order of the synteny blocks detected between all genomes? This is why I was looking at reconstruct but it looks like it's looking at the order of WGD, but in my case I'm interested in small singleton chromosomes of bacteria with the occasional plasmids.