Should we remove plasmid sequences for Whole genome Alignment

Question

[Optimist]

Hello there!!

Should we remove plasmid sequences from genome assemblies for Whole Genome alignment?

I want to perform Whole genome alignment among 20 bacterial genomes. of 20, only 5 genomes have plasmids in them while the rest have only chromosome.

Is it advisable to remove those plasmid sequences before proceeding to Whole genome alignment using Progressive mauve?

Thank You

[shenwei356]

Better remove them cause plasmids are highly mobile elements.