I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequence is contained in the larger), and DCJ-Indel (which counts number of rearrangements and large indels distinguishing two plasmids). It uses these distances to build a relationship network, and various visualisations of this network are part of the output! First an initial containment network is built where each node is a plasmid, and an edge between two plasmids/nodes is added if at least 50% of the smaller one is contained in the larger. Then we induce a subnetwork on this containment network, in which we remove any edge that has DCJ-Indel distance greater than 4. You can think of it like this: plasmids will share an edge if they have enough sequence in common, and don't have a lot of structural changes between them. We use the initial containment network to assign a broad community based on containment distances, and then the DCJ-Indel subnetwork to assign a tighter subcommunity based on both containment and DCJ-Indel distances. The distances we use means that the tool copes very well with differences in size. The documentation in the github will have some more details on the approach.
We've found that generally the subcommunities the tool produces tend to have a reasonable amount of core genes, so you can even still do a classic core gene phylogeny on top of it.
It is still a work in progress, so installation might be a little clunky and documentation isn't quite finished, but we've had a couple of people use it and they've found it okay, and I am more than happy to answer any questions! Since you have already isolated each plasmid into an individual fasta file, all you'd need to do is install the tool, and then you'd be good to go.
Can you roughly subdivide them into groups based on their size? I assume these bacterial strains are a single organism (or closely related)? Then you could use roary on the groups of plasmids to generate the trees.
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reasonable work-flow and thought I better ask for advice. Yes, all of these bacterial strains are a single organisms (Enterococcus faecium). I have been thinking of trying this but have several questions:
1) If plasmids are similar in size but a different plasmid family - will this impact the core-gene plasmid output? I.e. if they are quite diverse even if they are similar in size? 2) What would you consider is a reasonable division based on size? Would plasmids ranging from 2,000-20,000 bp, 30,000-90,000 and 100,000-200,000 be too large of a division?
Thank you again, I really appreciate the advice.
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a wide range so criteria for classification may need to be chosen in a way that makes biological sense.
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as the size range tend not to be quite as large (e.g, one core phylogeny for rep11a types etc). Hopefully this makes sense. Thank you for your help! My final year PhD brain was ready to burst :)