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Table 2 Effects of MaxAlign and removal of gapped columns on phylogenetic accuracy

From: MaxAlign: maximizing usable data in an alignment

MaxAlign Removal of gaps Set of taxa used for comparison Tree 1 Tree 2 Tree 3
- - Subset 85.9 (0.5) 85.4 (0.2) 78.7 (0.3)*
- + Subset 21.0 (0.5) 60.1 (0.4) 49.1 (0.4)
+ - Subset 82.8 (0.6) 82.3 (0.2) 78.6 (0.3)*
+ + Subset 74.6 (0.7) 75.9 (0.3) 72.4 (0.3)
- - All 56.1 (0.5) 78.4 (0.2) 79.7 (0.3)
- + All 10.3 (0.2) 52.7 (0.4) 53.2 (0.4)
  1. Phylogenetic accuracy for datasets with/without removal of gapped columns, and processed/not processed by MaxAlign. Accuracy is measured as the average normalized symmetric tree similarity between the true tree (used for simulating data) and the individual inferred trees, with the standard error of the mean (in %) given in parenthesis. "Subset" refers to the set of taxa (sequences) common to the original and the MaxAligned data. "All" means all taxa in the original data set. Values marked with * are the only ones whose difference is not statistically significant.