I have approximately bacterial 40 (non conserved) genes in which I am interested, I want to build a phylogenetic tree per gene (so 40 trees) and later I want to (try) take a consensus tree of that. All of the genes are around 200-500bp. I have installed raxml, iqtree and megax, and I can work with all of them. But, because I don't have a lot of theoretical background on phylogeny I was wondering if anyone has any suggestions or could help me by explaining or sending me relevant theory. Of course I have looked on google and in the manuals of the software I listed but I couldn't really find what I was looking for.
Basically my questions are:
Is there a "best" way to build phylogenetic trees based on one bacterial gene?
Is there a software that allows you to use all 40 genes as input and generates just one tree from that?
Thanks a lot!