Figure 5.

Accuracy of species tree estimation, eight-species-trees. For larger trees, only PoMo, STEM + UPGMA, and concatenation with MrBayes or HyPhy could be used. Eight species and 10 samples per species were included. The Y axis is the error in species tree estimation calculated as BSD between the normalized simulated species tree and the normalized estimated tree, the X axis is the number of genes included in the analysis. Each boxplot includes 10 independent replicates. Different colors represent different methods (see legend). a) $1N_e$ tree height and balanced tree. b) $1N_e$ tree height and unbalanced tree. c) $10N_e$ tree height and balanced tree. d) $10N_e$ tree height and unbalanced tree. PoMo performs much better than STEM + UPGMA, and is slightly more accurate than the two concatenation approaches.