Pathogen outbreak study - Pseudomonas single isolate WGS

We have been analysing the data you sent us and its looking really good. We are trying to do some additional analyses and hope you can assist.

• We would like to extract the in silico MLST profiles from these genomes.
• Reconstruct the phylogenetic tree to include certain outgroups (Burkholderia cepacia, Pseudomonas fluorescens, Pseudomonas putida). This will allow us to root the tree and get a better context for evolution.
• Are you able to assist constructing a phylogenetic heatmap (see image below) or even 2-dimensional? This would include the phylogenetic data on one side, and some additional data, such as presence of certain genes, etc. on the other?
• For the plasmid resistome results, we have found hit which is present in all the outbreak isolates and only a few of the non-outbreak isolates. The gene fractions for these results only go up to approximately 60%. Does this mean that only 60% of the reference plasmid is covered? If so, is the rest of the plasmid unique, or perhaps absent? We would like to compare this plasmid from all the isolates to see how similar they are to the reference (CP002153.1) as well as to each other. Can you assist with plasmid assembly and constructing a plasmid map (see below)?
• For the virulence factors we have identified 3 factors (NP_253217, NP_251844, NP_251850) present in all the outbreak isolates and only a few of the non-outbreak isolates. Could you extract these sequences from the relevant contigs and blast, and do a multiple alignment for comparison of each one? These factors confer different levels of virulence depending on the mutations present.