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Table 2 Condensed rankings for methods in Table 1 with additional performance numbers

From: Looking for trees in the forest: summary tree from posterior samples

Method TIMES CME CCE MODEL POLY MF% CAE% CME%
CAT,TCB 1 1 14 19 0.0% 45.2% 3.79% 36.33%
CAT,MCC 2 4 15 18 0.0% 45.3% 3.79% 36.46%
TP (avg) 5 0 13 11 0.0% 93.2% 4.37% 36.22%
TP (med) 12 0 12 1 0.0% 98.6% 4.50% 36.21%
SRBS,TCB 6 8 7 12 4.1% 91.8% 4.38% 36.64%
MED,TCB 7 3 9 8 1.1% 94.0% 4.36% 36.36%
HSO,TCB 8 2 10 10 1.1% 94.0% 4.36% 36.35%
MED,MCC 9 6 13 6 0.9% 94.6% 4.37% 36.48%
mSRBS 9 9 8 9 3.8% 92.1% 4.39% 36.80%
HSO,MCC 10 5 14 7 0.9% 94.6% 4.37% 36.48%
AVG,MCC 10 7 11 13 1.1% 84.2% 4.30% 36.49%
SRBS,MCC 11 10 8 11 4.2% 91.9% 4.39% 36.8%
mHS 0 19 1 16 29.8% 50.0% 3.97% 44.48%
HS,MCC 3 19 2 14 34.3% 54.9% 4.16% 44.27%
HS,TCB 4 18 2 15 34.5% 54.6% 4.18% 44.09%
CONS (med) 6 17 0 17 27.5% 46.3% 3.98% 43.00%
RAS,MCC 13 15 6 3 24.4% 93.1% 4.66% 42.45%
RAS,TCB 14 14 5 4 24.2% 92.7% 4.67% 42.26%
mRAS 15 16 6 5 24.5% 88.2% 4.74% 42.73%
RBS,TCB 16 11 4 2 23.4% 99.0% 4.82% 40.60%
mRBS 17 12 3 0 23.8% 99.1% 4.84% 40.80%
RBS,MCC 18 13 5 0 23.7% 99.0% 4.81% 40.94%
  1. The ranks for RH, CAE and DVE were added to make the TIMES rank indicating fit of clade heights, and MF, TLL and CLL ranks added to make MODEL rank indicating fit of topology. The POLY column shows the mean number of branches with length zero, which effectively create a polytomy in the tree. The number of zero length branches in each tree were divided by the total number of branches to turn them in percentages so that they can be averaged over all 2000 test cases. The MF% column shows the mean percentile of the summary tree log-likelihood (tree+coalescent) in the posterior samples. For example, a value of 94% means that the summary tree log-likelihood was higher than 94% of the posterior trees. The CAE% column show the mean clade age errors per clade, as a percent of tree height. The CME% column shows the mean number of missed clades, as a percentage of the number of non-trivial clades in the tree. The means are obtained by averaging the statistic over the 2000 summary trees produced by each method.