I want to generate a phylogenetic tree based on bacterial core/essential genes.
I stumbled over bcgTree ( https://github.com/molbiodiv/bcgTree ). Did anyone try it already? If yes, what do you like/dislike? Do you have an opinion on if it produces "paper ready" results (to me it looks good...)
If you don't like it for some reason, what alternatives do you suggest (I mean methods or software doing phylogeny on essential genes to get a stable and reliable tree)? (Besides MLSA from manually picked genes as a fallback strategy)