Phylogenetic program | Trees a
| Loci b
| Monophyletic trees c
| Monophyletic loci d
| Infeasible e
|
|---|
PHYLIP | 76 | 1394 | 3 (3.9%) | 1115 (80.0%) | 35 40.8 |
BioNJ | 6298 | 125,928 | 5 (0.1%) | 63,013 (50.0%) | 366 5.8 |
PhyML | 6297 | 125,914 | 46 (0.7%) | 80,805 (64.2%) | 229 3.6 |
RAxML | 6298 | 125,928 | 34 (0.5%) | 73,576 (58.4%) | 213 3.4 |
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aThe number of gene trees considered for each program. For PHYLIP, since many trees were non-binary, we considered only trees for which we can definitively determine their reconciliation feasibility or infeasibility. In particular, non-binary trees with a reconcilable LEG were not considered. For PHYLIP and PhyML, one tree could not be reconstructed
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bThe number of species-specific loci across all trees
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cThe number and percentage of trees for which, for every species-specific loci, the genes in that loci were inferred to be monophyletic
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dThe number and percentage of species-specific loci for which the genes in that loci were inferred to be monophyletic
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eThe number and percentage of trees with infeasible reconciliations
