I wanted to make a phylogenetic tree using core genes from a number of bacterial strains. For this I had approximately 100 genomes, I used the annotated sequences and using a python script, I narrowed down the core genes for my 100 genomes. In the output, I got around 500 files, each file with a gene that is present in all 100 genomes. I concatenated all the genes for each strain and made a maximum likelihood phylogenetic tree. Now I would like to have a heat map next to my phylogenetic tree that would show color coding for different variations in the genes that I used to construct the phylogenetic tree. Is there a way I can do this, or is there any other approach to do this?