Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
Figure 1
Comparison of tree distance metrics for topology pairs over 64 taxa.
The vertical bars represent the 95% range, and diamonds intercept the median over 5000 replicates for each simulated distance. The cMAST estimates (black) were calculated with PAUP [33], while the Robinson-Foulds (RF) distance (gray) and our d̂SPR approximation (blue) were computed using in-house software. The diagonal line (red) represents the case where the estimate and true values agree. On the horizontal axis, we have the “real” number of SPR moves applied (ranging from one to 16) on random topologies, and, on the vertical axis, we show the estimated distances using the RF, cMAST and d̂SPR methods.