Fig 2. Topology accuracy of RAxML, TreeFix and ProfileNJ trees, measured by RF distance with the true tree, on ∼ 2500 simulated trees from the fungal dataset.
We use a sample of trees simulated under four different DL rate: (1rD—1rL), (2rD—2rL), (4rD—4rL) and (4rD—1rL). Percentage of reconstructed trees (y-axis) with a given RF distance (x-axis) to the true tree. TreeFix and ProfileNJ have a similar reconstruction accuracy (75% of trees match the true trees) while the input trees (RAxML) have the lowest accuracy. The graph is cut on the right, but contains more than 99% of the data.