Table 3 Parameters varied in the simulations

Data set

S:

small

L:

large

Taxa coverage

c:

complete

m:

missing

True gene trees

E:

subtrees of species tree

R _α :

rate of evolution assigned randomly from a Γ-distribution with parameter α (i.e., mean 1 and variance 1/α )

P:

substitution parameters and branch lengths gene-specific

G:

trees gene-specific

T _θ :

trees random by coalescent process with parameter θ

Reconstructed

e:

equal to true gene trees

gene trees

n:

normal sequence length and ML estimation