I generated a phylogenetic tree based on the GTDB database using phyloT (phyloT: Help), which uses bacterial reference tree when creating a pruned version. The GTDB based trees (generated by phyloT) are proper phylogenetic reference trees, containing branch lengths and clade support. I would like to know the unit of the scale bar that is present in the phylogenetic trees generated in this manner using GTDB.
Hi. The GTDB reference trees are standard maximum-likelihood trees inferred with FastTree for Bacteria and IQ-Tree for Archaea. Branches are thus expected number of substitutions per site. Additional information of the methods used by GTDB can be found on the website: GTDB - Methods.