Table 1.

Reconciliation infeasibility in apes data set

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

^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

^bThe number of species-specific loci across all trees

^cThe number and percentage of trees for which, for every species-specific loci, the genes in that loci were inferred to be monophyletic

^dThe number and percentage of species-specific loci for which the genes in that loci were inferred to be monophyletic

^eThe number and percentage of trees with infeasible reconciliations