Experiments results. Running times for the eight experiments. Experiment 1: rate matrix estimation using EM. The plot shows the running time for calculating the statistics for each method, as a function of the number of sequences included in the data set. For experiments 2 and 3 we calculated the value of Σ(C;t
) for 10 time points t
. Each plot starts with the running time of the precomputation and at position k we plot the cumulative running time for precomputation and the evaluation of Σ(C;t
) for all t
}. The values of t
are provided in Table 2. Experiment 4: robust distance estimation. The plot shows the running time for computing the robust distance as a function of the evolutionary distance t. Experiments 5-8: similar as for experiments 2 and 3 but with a GTR model (experiments 5 and 6) and UNR model (experiments 7 and 8) instead of a GY model.