Table 2

Effects of MaxAlign and removal of gapped columns on phylogenetic accuracy

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)


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.

Gouveia-Oliveira et al. BMC Bioinformatics 2007 8:312   doi:10.1186/1471-2105-8-312

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