In this dataset, no only amino acid substitutions at a fixed rate are modeled. This is the base case for any further analysis.
| Disturbance | Vertabrate-like Tree | Bacteria-like Tree | ||||
|---|---|---|---|---|---|---|
| Tree 1 | Tree 2 | Tree 3 | Tree 1 | Tree 2 | Tree 3 | |
| n/a | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 | Repl 1 Repl 2 Repl 3 Repl 4 Repl 5 |
In addition to amino acid substitutions, for these datasets the gene duplication rate is varied (in percent of affected genes in the present day genomes) and also the loss rate (given as the ratio of loss rate and duplication rate).
On these datasets we model different rates of lateral gene transfers with orthologous replacement.
On these datasets we model errors in the sequencing step. We replace a random fraction of positions with other amino acids.
For these datasets we varied the insertion/deletion rate during the evolution.