Accuracy of transfer events detection. A: numbers of true positive LGTs (TP). B: numbers of false positive LGTs (FP). LGT events detected in maximum-likelihood gene trees are displayed as a function of the real number of transfers per tree. Results were computed with a support threshold for topological conflict significance of 0.90. As EEEP and RIATA-HGT may propose multiple scenarios, grey areas represent the variability between the worst and the best scenarios. Areas are delimited by blue borders for RIATA-HGT and green borders for EEEP. Prunier (fast version) results are drawn in magenta. The black curves symbolize the reference boundary: those curves were obtained using RIATA-HGT (best scenario selected) on true gene trees (before sequence simulation). The green numbers below the true positives area of EEEP represent the number of unresolved cases (either quoted as "Unsolved" by the program, or resulting from a program crash). The blue numbers above RIATA-HGT TP area indicate the two cases for which the program crashed. A program crash is counted as 0 TP and 0 FP. The grey line shows a relationship 1:1 between the two axes. The estimated number of transfers by each method is the sum of the curves shown in A and B.