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Table 2 Comparison of different algorithms

From: Towards a practical O(n logn) phylogeny algorithm

   data set     
  COG1011 COG840 COG1028
  250 sequences 1250 sequences 5000 sequences
method % taxa RF QA % taxa RF QA % taxa RF QA
weighted majority, 5 quartets 88.5 66.2 72.8 84.1 57.4 85.8 74.4 51.4 59.5
WTA-vote, 5 quartets 86.0 69.4 70.8 80.2 62.3 85.4 70.1 57.0 59.6
weighted majority, 20 quartets 95.6 60.4 69.9 96.4 50.6 83.9 94.3 41.1 56.5
WTA-vote, 20 quartets 94.0 69.4 73.4 92.1 60.8 83.1 89.7 57.6 55.3
NJ 100 73.6 70.0 100 62.6 88.0 100 73.0 66.3
FastTree (NJ phase only) 100 69.7 85.9 100 61.0 86.6 100 73.6 66.4
weighted majority, 5 quartets, force all taxa 100 59.0 69.7 100 48.7 80.8 100 37.3 52.4
  1. Performance of the random walk algorithm on synthetic alignments. The size of the guide tree was 200 except for the 250 taxon data set, where it was set to 100. The average RF accuracy of the guide trees was 65,50, and 46% for the 250,1250, and 5000-taxon data sets, respectively. The average quartet accuracies for the guide trees were 73,83 and 55%. When all taxa are forced into the random walk tree (see text), the RF accuracy decreases by 7 − 14%, depending on the data set. All random walk runs use the confidence threshold heuristic and two additional rounds of insertions.