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Table 2 Average running time of 10 runs of each algorithm, for different tree diameters in two different simulated datasets.

From: Reconstruction of ancestral gene orders using intermediate genomes

Dataset

20 genomes, 500 genes

12 genomes, 5000 genes

Diameter

D= 1n

D= 2n

D= 3n

D= 4n

D= 1n

D= 2n

D= 3n

D= 4n

SCJ

3 s

3 s

4 s

4 s

7 s

9s

11 s

11 s

PATHGROUPS

18 s

40 s

57 s

1 m18 s

22 m16 s

1 h21 m42 s

1 h16 m34 s

31 m13 s

GASTS

22 s

1 m6 s

2 m46 s

4 m41 s

1 h14 m6 s

12 h27 m13 s

19 h8 m55 s

22 h2 m32 s

ProCARs

14 m9 s

30 m10 s

36 m28 s

1 h9 m5 s

-

-

-

-

IG-Pure

2 s

3 s

3 s

3 s

1 m38 s

2 m23 s

2 m44 s

1 m53 s

IG-SCJ

2 s

3 s

4 s

4 s

1 m4 s

1 m41 s

2 m8 s

1 m26 s

IG-ProCARs

3 s

3 s

4 s

4 s

-

-

-

-

  1. In the combined IG algorithms, only the IG time is shown, without the homology method time (SCJ or ProCARs). Also, for the IG-methods ran as distance-based algorithms, the time is roughly 50× more, since the algorithms were repeated 50 times and the smallest tree was chosen.