Maybe this is a very basic question but I can’t figure out the answer to it. I’m using genomic alignments to run ML inference with RAxML. Among my alignments, I have several species that I’d like to use as outgroup species. There is the option, on RAxML, to define a priori which species are your outgroup and then generate a rooted tree. I know it is possible to root trees a posteriori (e.g. package ape on R), so I was wondering what is the advantage of defining an outgroup a priori. Will this have any influence on tree inference and/or the ML algorithm?