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Table 1 Inferred values of α, the parameter of the discrete gamma distribution of the rates across sites, inferred weight of one of the two components (w) and Pearson correlation (r) of the inferred tree branch lengths with the true ones of their respective component, for sequences simulated with various values for τ and α.

From: Evaluation of the models handling heterotachy in phylogenetic inference

α/w/r

Ď„ = 0.2

Ď„ = 0.4

Ď„ = 0.6

Ď„ = 0.8

α = 0.5

0.51/0.028/n.a.

0.52/0.42/0.976

0.49/0.46/0.993

0.52/0.50/0.998

α = 1.0

1.06/0.033/n.a.

1.04/0.43/0.993

1.00/0.47/0.993

1.02/0.49/0.998

α = 1.5

1.51/0.07/n.a.

1.56/0.50/0.993

1.56/0.48/0.997

1.46/0.49/0.998

α = 2.0

2.01/0.005/n.a.

2.04/0.41/0.979

1.89/0.49/0.999

1.99/0.50/0.998

  1. Note that the correlation between the true branch lengths of the two components are 0.86, 0.52, 0.19 and -0.16 with Ď„ = 0.2, 0.4, 0.6 and 0.8, respectively. Two components were used for the inference. When Ď„ = 0.2, the partition identity cannot be recovered, so the branch lengths cannot be compared with the true ones.