Hi all,
I am trying to compare a few bacterial genomes from several different distinct taxonomic groups in order to see if I am able to identify any signature genomic regions within these groups. Unfortunately, I am not really familiar enough with phylogenetic analysis to know of a way to do this efficiently. I have tried using Gview already but the results are not easy to quantitatively interpret (or at least with the dataset size I am trying to work with...).
Essentially, I have 7 different taxonomic groups with between 5-20 genomes in each group (currently I have the genbank formatted annotation) and just want to identify signature components of the genome for future identification purposes (as in, genomic regions that are conserved in the ingroup and excluded in the outgroup).
Any advice would be greatly (and desperately) appreciated.
Maybe this article can help (Not bacteria, but the method section and using rRNA genes to create the phylogenetic tree might help):
https://aem.asm.org/content/aem/82/16/4921.full.pdf