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Table 3 Branch-lengths-from-reconstruction versus Tree-branch-length

From: Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

 

Branch-lengths-from-reconstruction*

Tree-branch-length

 
  

0

.0001 – .006

.0061 – .020

.0201 – .040

.0401 – .070

.0701 – .130

.1301 – .220

.2201 – .400

.4001 – 1.00

≥ 1.001

 

AF

            
 

0

5,891

1,292

6

4

0

0

0

0

0

3

7,196

 

.0001 – .006

412

16,365

2,268

129

66

29

1

1

0

10

19,281

 

.0061 – .020

130

1,576

11,110

1,829

100

93

47

1

2

12

14,900

 

.0201 – .040

99

410

2,406

7,070

2,456

146

80

31

1

1

12,700

 

.0401 – .070

145

274

1,591

2,795

7,045

3,475

125

66

5

5

15,526

 

.0701 – .130

191

221

1,555

3,717

4,645

11,268

5,841

305

33

1

27,777

 

.1301 – .220

169

89

474

1,673

3,396

5,753

10,051

10,022

583

4

32,214

 

.2201 – .400

100

28

88

237

666

1,866

2,848

8,811

14,136

626

29,406

 

.4001 – 1.00

10

1

2

3

8

48

63

178

2,492

3,507

6,312

BF

            
 

0

7,131

7,791

1,260

295

137

103

51

23

8

7

16,806

 

.0001 – .006

11

11,570

4,748

1,282

575

275

90

28

15

13

18,607

 

.0061 – .020

0

883

12,873

9,119

4,506

2,641

883

232

51

19

31,207

 

.0201 – .040

0

10

606

6,487

8,980

5,554

2,046

779

175

13

24,650

 

.0401 – .070

0

1

12

269

4,067

10,172

4,592

1,770

559

60

21,502

 

.0701 – .130

1

0

0

5

115

3,887

10,244

8,278

2,757

252

25,539

 

.1301 – .220

0

0

0

0

2

46

1,142

7,954

8,907

1,043

19,094

 

.2201 – .400

4

0

0

0

0

0

7

350

4,737

2,175

7,273

 

.4001 – 1.00

0

1

1

0

0

0

1

1

43

587

634

BC

            
 

0

7,142

17,555

2,581

405

173

128

71

30

10

13

28,108

 

.0001 – .006

0

0

0

0

0

0

0

0

0

0

0

 

.0061 – .020

0

2,683

15,870

7,557

1,317

340

122

59

21

13

27,982

 

.0201 – .040

0

16

988

8,382

7,874

1,731

277

77

17

5

19,367

 

.0401 – .070

0

1

60

1,074

8,310

9,621

1,240

217

46

6

20,575

 

.0701 – .130

0

0

0

38

698

10,587

11,484

2,207

264

13

25,291

 

.1301 – .220

0

0

0

1

10

270

5,813

13,177

2,598

36

21,905

 

.2201 – .400

5

0

0

0

0

1

48

3,646

13,213

1,120

18,033

 

.4001 – 1.00

0

1

1

0

0

0

1

2

1,083

2,963

4,051

  1. *Replacements per site from all fractional (AF), best fractional (BF), and best count (BC) tools.