Table 1 Results of Look4LTRs, LTR_Finder, LTRharvest, and LtrDetector on the training and testing genomes. GT is the number of elements in the ground truth, TP is the number of true positives, FP is the number of false positives, Total Predictions is the number of predictions made by a tool, memory is the peak memory usage of a tool, and time is the total time taken by a tool to run. ^aWe did not run LTR_Finder on Zea mays due to the time it would take. ^bFor the overall peak memories, we take the maximum peak memory usage from each tool over the training genomes. Note that LTRharvest and LTR_Finder were run as provided by their authors — without parallelization — because a biologist would apply them this way without any modifications

Arabidopsis thaliana

     Look4LTRs

86.67

91.23

88.89

120

104

10

2,381

4.62

00:00:54

     LTR_Finder

42.50

100.00

59.65

120

51

0

386

0.92

01:02:38

     LTRharvest

81.67

97.03

88.69

120

98

3

1,787

0.24

00:01:56

     LtrDetector

89.17

89.17

89.17

120

107

13

2,436

6.12

00:02:20

Oryza sativa japonica

     Look4LTRs

90.80

92.78

91.78

1,500

1,362

106

10,462

12.94

00:01:51

     LTR_Finder

60.47

99.13

75.11

1,500

907

8

5,061

0.95

05:51:45

     LTRharvest

72.67

91.37

80.95

1,500

1,090

103

6,684

0.34

00:05:54

     LtrDetector

86.87

85.67

86.26

1,500

1,303

218

1,0659

15.61

00:05:44

Glycine max

     Look4LTRs

87.03

99.06

92.66

1,573

1,369

13

34,229

15.35

00:12:16

     LTR_Finder

58.30

99.57

73.54

1,573

917

4

11,401

2.16

11:36:37

     LTRharvest

78.70

99.52

87.89

1,573

1,238

6

21,074

0.45

00:23:07

     LtrDetector

89.57

95.14

92.27

1,573

1,409

72

37,956

26.36

00:09:58

Sorghum bicolor

     Look4LTRs

88.11

97.09

92.38

5,519

4,863

146

36,945

15.25

00:04:04

     LTR_Finder

53.47

98.63

69.35

5,519

2,951

41

12,333

1.72

05:14:25

     LTRharvest

58.04

91.10

70.90

5,519

3,203

313

18,882

0.60

00:11:16

     LtrDetector

81.75

93.59

87.27

5,519

4,512

309

34,682

15.78

00:29:45

Training Overall

     Look4LTRs

88.36

96.55

92.27

8,712

7,698

275

84,017

15.35^b

00:15:53

     LTR_Finder

55.39

98.91

71.02

8,712

4,826

53

28,181

2.16^b

23:45:25

     LTRharvest

64.61

92.98

76.24

8,712

5,629

330

48,427

0.6^b

00:42:13

     LtrDetector

84.15

92.30

88.03

8,712

7,331

612

85,733

26.36^b

00:47:47

Zea Mays

     Look4LTRs

89.14

99.50

94.03

12,697

11,318

57

158,819

35.67

00:18:24

     LTR_Finder^a

–

–

–

–

–

–

–

–

–

     LTRharvest

58.26

99.74

73.55

12,697

7,397

19

85,298

2.35

00:34:34

     LtrDetector

82.52

98.47

89.79

12,697

10,478

163

150,343

23.15

00:29:47

Solanum lycopersicum

     Look4LTRs

82.60

99.21

90.14

454

375

3

26,789

14.73

00:03:48

     LTR_Finder

37.00

100.00

54.02

454

168

0

3,534

1.30

06:17:42

     LTRharvest

86.78

99.49

92.71

454

394

2

18,751

0.70

00:09:03

     LtrDetector

84.36

99.48

91.3

454

383

2

26,715

16.90

00:17:08

Solanum tuberosum

     Look4LTRs

89.12

86.00

87.54

524

467

76

27,156

10.92

00:06:05

     LTR_Finder

19.85

84.55

32.15

524

104

19

2,498

1.24

07:11:49

     LTRharvest

81.68

86.64

84.09

524

428

66

21,358

0.61

00:07:59

     LtrDetector

79.77

70.85

75.04

524

418

172

36,179

17.56

00:17:03

Theobroma cacao

     Look4LTRs

77.65

97.62

86.50

264

205

5

13,035

7.16

00:02:52

     LTR_Finder

22.73

100.00

37.04

264

60

0

1,784

0.54

03:36:37

     LTRharvest

69.32

99.46

81.70

264

183

1

7,071

0.32

00:04:18

     LtrDetector

77.65

98.56

86.86

264

205

3

12,796

12.63

00:06:32