Method | Data set | Tree Figure | Ectoprocta+Phoronida | Ectoprocta+Entoprocta | Ectoprocta+Annelida | Ectoprocta+Gastropoda | Brachiopoda+Annelida | Phoronida+Nemertea | Phoronida+Entoprocta |
---|---|---|---|---|---|---|---|---|---|
Maximum-likelihood (MtZoa+F model) | Amino acid data set, with Lingula | Additional file 2 | Â | Â | Â | Â | Â | Â | <50 |
Maximum-likelihood (GTR model) | Nucleotide data set | Additional file 3 | Â | Â | Â | <50 | 86 | <50 | Â |
Maximum-likelihood (GTR model) | Nucleotide data set (Gblocks edited) | Additional file 4 | Â | Â | Â | Â | <50 | Â | Â |
Maximum-likelihood (GTR model) | Nucleotide data set (direct nucleotide alignment) | Additional file 5 | Â | Â | Â | Â | 99 | Â | Â |
Maximum-likelihood (MtZoa+F model) | Amino acid data set | Additional file 6 | Â | Â | Â | Â | 52 | Â | 52 |
Maximum-likelihood (MtZoa+F model) | Amino acid data set (Gblocks edited) | Additional file 7 | Â | Â | Â | <50 | Â | <50 | Â |
Maximum-likelihood (GTR model) | 1st and 2nd codon positions | 5B | Â | Â | Â | <50 | <50 | <50 | Â |
nhPhyML | Nucleotide data set; starting tree GTR tree | Additional file 8 | Â | Â | Â | x | Â | x | Â |
nhPhyML | Nucleotide data set; starting tree CAT tree | Additional file 9 | x | Â | Â | Â | Â | Â | Â |
Bayesian (CAT model) | Amino acid data set | 5A | Â | Â | 0.84 | Â | Â | Â | Â |
Bayesian (CAT model) | Amino acid data set; 10 taxa with the most strongly differing amino acid composition excluded | Additional file 11 | Â | Â | 0.78 | Â | Â | Â | 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 | Â | <50 | Â | Â | <50 | Â | Â |
Bayesian (CAT model) | Amino acid data set recoded using 9 minmax chi-squared bins' | Additional file 14 | Â | Â | 0.92 | Â | Â | Â | Â |
Maximum-likelihood (MULTIGAMMA model) | Amino acid data set recoded using 9 minmax chi-squared bins | Additional file 15 | Â | Â | Â | Â | 60 | Â | Â |
Bayesian (CAT model) | Amino acid data set recoded using 6 minmax chi-squared bins | Additional file 16 | Â | Â | Â | Â | 0.96 | Â | Â |
Maximum-likelihood (MULTIGAMMA model) | Amino acid data set recoded 6 minmax chi-squared bins | Additional file 17 | Â | Â | Â | Â | <50 | Â | <50 |
Bayesian (CAT model) | Amino acid data set recoded using Dayhoff groups | Additional file 18 | Â | Â | Â | Â | Â | Â | Â |
Maximum-likelihood (MULTIGAMMA model) | Amino acid data set recoded Dayhoff groups | Additional file 19 | Â | Â | Â | Â | Â | Â | <50 |
Bayesian (CAT+BP model) | Amino acid data set | Additional file 20 | Â | Â | 0.63 | Â | Â | Â | Â |
Maximum-likelihood (GTR model) | Nucleotide data set, 20% of the alignment positions with highest sitewise rates removed | Additional file 21 | Â | Â | Â | Â | 98 | Â | Â |
Maximum-likelihood (MtZoa+F model) | Amino acid data set; 10% of the alignment positions with highest sitewise rates removed | Additional file 22 | Â | Â | Â | Â | <50 | Â | 58 |