Plasmid Phylogeny from Whole genome sequencing

Question

[karthick.1087]

Is there any way to construct phylogenetic tree of plasmids from whole genome sequencing? Please suggest the tools or methods for the same

Answer 1

[gayachit]

The best would be to sequence the plasmids and do a phylogeny but if you only have whole genome data, I think you would have to extract the plasmid sequences using tools like plasmid finder or plasmid seeker and do a phylogeny the same way as any other using tools like MEGA and MAFFT etc. For reference : https://www.frontiersin.org/articles/10.3389/fmicb.2018.02167/full#h3