Table 4 Phylogenetic relationships of ectoprocts, brachiopods and phoronids according to different phylogenetic analyses (only sister group relationships with one other phylum; more complex relationships are not considered).

Maximum-likelihood (MtZoa+F model)

Amino acid data set, with Lingula

Additional file 2

<50

Maximum-likelihood (GTR model)

Nucleotide data set

Additional file 3

<50

86

<50

Maximum-likelihood (GTR model)

Nucleotide data set (Gblocks edited)

Additional file 4

<50

Maximum-likelihood (GTR model)

Nucleotide data set (direct nucleotide alignment)

Additional file 5

99

Maximum-likelihood (MtZoa+F model)

Amino acid data set

Additional file 6

52

52

Maximum-likelihood (MtZoa+F model)

Amino acid data set (Gblocks edited)

Additional file 7

<50

<50

Maximum-likelihood (GTR model)

1^st and 2^nd codon positions

5B

<50

<50

<50

nhPhyML

Nucleotide data set; starting tree GTR tree

Additional file 8

x

x

nhPhyML

Nucleotide data set; starting tree CAT tree

Additional file 9

x

Bayesian (CAT model)

Amino acid data set

5A

0.84

Bayesian (CAT model)

Amino acid data set; 10 taxa with the most strongly differing amino acid composition excluded

Additional file 11

0.78

0.58

Maximum-likelihood (MtZoa+F model)

Amino acid data set; 10 taxa with the most strongly differing amino acid composition excluded

Additional file 12

<50

<50

Bayesian (CAT model)

Amino acid data set recoded using 9 minmax chi-squared bins'

Additional file 14

0.92

Maximum-likelihood (MULTIGAMMA model)

Amino acid data set recoded using 9 minmax chi-squared bins

Additional file 15

60

Bayesian (CAT model)

Amino acid data set recoded using 6 minmax chi-squared bins

Additional file 16

0.96

Maximum-likelihood (MULTIGAMMA model)

Amino acid data set recoded 6 minmax chi-squared bins

Additional file 17

<50

<50

Bayesian (CAT model)

Amino acid data set recoded using Dayhoff groups

Additional file 18

Maximum-likelihood (MULTIGAMMA model)

Amino acid data set recoded Dayhoff groups

Additional file 19

<50

Bayesian (CAT+BP model)

Amino acid data set

Additional file 20

0.63

Maximum-likelihood (GTR model)

Nucleotide data set, 20% of the alignment positions with highest sitewise rates removed

Additional file 21

98

Maximum-likelihood (MtZoa+F model)

Amino acid data set; 10% of the alignment positions with highest sitewise rates removed

Additional file 22

<50

58