Go to GitHub directory.
Trees of individual marker genes were reconstructed using RAxML under the CAT model, with the optimal amino-acid substitution model selected per gene. Branch lengths were further optimized using either RAxML or IQ-TREE (if RAxML cannot complete) under the Gamma model.
Note that each tree typically contains a large proportion, but not all, of the 10,575 taxa, due to the absence or undetectability of the gene in the corresponding genome. The domains Bacteria and Archaea are not always perfectly separated, either. Therefore the trees are presented in the unrooted form.
Metrics of the trees are provided in the metadata of the 400 marker genes.