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Table 3 Robinson-Foulds distance between pairs of trees estimated using a range of methods

From: On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

Database

COG

TRIBES

OFAM

CL/SHOT

30

74

89

CL non-phylo/SHOT

22

60

58

CL phylo/SHOT

32

n/a

n/a

CL/RNA

44

60

63

CL non-phylo/RNA

46

45

62

CL phylo/RNA

46

n/a

n/a

SHOT/RNA

42

82

74

  1. CL (conditioned logdet); CL non-phylo (conditioned logdet with non-phylogenetic mixture model); CL phylo (conditioned logdet with phylogenetic mixture model); SHOT (SHOT distances and BIONJ); RNA (16S rRNA and PHYML). Distances marked n/a were not calculated because the phylogenetic mixture model was only applied to the COG dataset.