Help with phylogenetic analysis

Question

[KaTi]

Hi! I'm just starting out in this kind of data analysis and I wanted to ask you if you could tell me how I can start. namely, I would like to compare a certain cluster involved in the production of a compound in bacteria, and it is the case that in my bacteria and other related bacteria there is not one gene that is present in others and at the same time interacts with the gene next to it in the operon. I would like to download proteobacterium genomes and check which ones contain it and which ones do not, and make a phylogenetic tree to check at what point it was removed. Do you have any pipeline tips on how to do this?

Answer 1

[Mensur Dlakic]

For gene clusters studies on a large scale, I recommend:

https://github.com/gamcil/cblaster

Main GitHub pate lists a couple of published papers that explain everything in detail.