Note: All three models (standard, recombination and structured) have 40 sequences with a fixed number of mutations of 100. 10,000 repetitions were run for each model. For the model with recombination, the scaled recombination parameter was set to 5 for all programs and the number of recombining segments was set to 1000 for eggcoal and ms (CoaSim does not require this parameter). For the structured model, 4 populations of 10 samples with a migration rate of 1 were simulated. The populations joined 10 coalescent time units in the past.