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Table 1 Statistics of the WGDdetector performance on the test data

From: WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

Software

Date type

Clean genes

Number of threadsa

Elapsed time (hour)b

Max memory used (Gb)

Number ofsub-gene familiesc

ADHoRe

A. thaliana (genome)

27,301

15; 1

1.79 (1.05 + 0.74)

0.94

6649

J. regia (genome)

32,436

15; 1

2.09 (1.23 + 0.86)

2.11

6127

P. trichocarpa (genome)

39,410

15; 1

4.18 (1.51 + 2.67)

2.52

22,676

X. laevis (genome)

41,073

15; 1

4.82 (2.24 + 2.58)

4.08

14,055

MCScanX

A. thaliana (genome)

27,301

15; 1

1.62 (1.05 + 0.57)

0.73

14,363

J. regia (genome)

32,436

15; 1

2.64 (1.23 + 1.41)

1.44

4333

P. trichocarpa (genome)

39,410

15; 1

2.21 (1.51 + 0.70)

1.56

21,643

X. laevis (genome)

41,073

15; 1

6.27 (2.24 + 4.03)

1.65

23,721

WGDdetector

A. thaliana (genome)

27,301

15

5.57

9.16

6729

A. thaliana (RNA-seq)

23,495

15

6.32

6.32

6072

J. regia (genome)

32,436

15

8.88

15.56

8504

P. trichocarpa (genome)

39,410

15

11.65

11.65

9818

P. trichocarpa (RNA-seq)

20,354

15

5.18

11.84

5191

X. laevis (genome)

41,073

15

19.23

35.46

9391

  1. aThe format of “15; 1” representing the number of threads when protein clustering and the dS calculating
  2. bThe format “S (X + Y)” represent the total elapsed time (S), the protein clustering elapsed time (X) and the dS calculating elapsed time (Y)
  3. cIn the software ADHoRe and MCScanX, all the homologous genes were recorded. In the WGDdetector pipeline, only the sub-gene families were recoded