You can draw trees using several biological data. Usually people use highly conserved proteins like ribosomal proteins, align them, select blocks of alignments and draw a tree using this data. Another option is rRNA or other markers like insertion sequences and more. You should take into account that evolution of proteins might be different from evolution of rRNA or non-coding DNA.
That being said, every tree you build is valid, it just represents the data you used to build it. Since you are dealing with closely related bacteria it might not be such a bad idea to use DNA rather than highly conserved proteins.
Another issue is the algorithm used by Mauve, I'm not familiar with it so I can't say anything about it. You should have a way to validate your tree so you could trust it.
Hope I helped.
5.6 years ago by
Asaf ♦ 8.3k