Table 1.

Names and short descriptions of the methods tested

Name	Brief description
Concat+Dist	Distance-based analysis of the concatenated alignment
Concat+ML	ML analysis of the concatenated alignment
SDM*add	SDM* run on the gene tree distance matrices (+ post-processing)
DistRadd	DistR run on the gene tree distance matrices (+ post-processing)
ERaBLEadd	ERaBLE run on the gene tree distance matrices
SDM*	SDM* run on the estimated distance matrices (+ post-processing)
DistR	DistR run on the estimated distance matrices (+ post-processing)
ERaBLE	ERaBLE run on the estimated distance matrices