I put about 200 staph aureus isolates through snippy and core snippy to get a full multiple sequence alignment. I then put the MSA through Gubbins (specifying an outgroup and using the raxml_model GTRGAMMA) in order to make a tree which removed SNPs potentially associated with recombination. I then loaded the tree file onto iTree of Life (iToL) and found that its topology was as expected.
However, when I looked at the branch labels, they ranged from about 1.0435 to 269.536072. As I made a MLT, I was expecting the branch units to be in "substitutions per site" and so be very small numbers. It's as if I have made a distance-based tree and the branch units are in SNPs.
Does anyone know what has happened here and how I can get the branch units to "substitutions per site"? I am new to bioinformatics so it could be something very simple. Would really appreciate any help I can get!