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Table 5 Parameters estimation and likelihood ratio tests for the branch-site models

From: Molecular cloning and expression analysis of WRKY transcription factor genes in Salvia miltiorrhiza

Branch-site model

Foreground branches

Estimates of parameter

Positive delection sites(BEB)

Site class 0

Site class 1

Site class 2a

Site class 2b

 

P0 = 0.10272

P1 = 0.36090

P2a = 0.11884

P2b = 0.41754

 

Group 1

ω0(b) = 0.05880

ω1(b) = 1.00000

ω2a(b) = 0.05880

ω2b(b) = 1.00000

None

 

ω0(f) = 0.05880

ω1(f) = 1.00000

ω2a(f) = 1.00000

ω2b(f) = 1.00000

 
 

P0 = 0.45646

P1 = 0.17985

P2a = 0.26089

P2b = 0.10279

 

Group 2a

ω0(b) = 0.05165

ω1(b) = 1.00000

ω2a(b) = 0.05165

ω2b(b) = 1.00000

None

 

ω0(f) = 0.05165

ω1(f) = 1.00000

ω2a(f) = 1.00000

ω2b(f) = 1.00000

 
 

P0 = 0.42991

P1 = 0.34434

P2a = 0.12535

P2b = 0.10040

 

Group 2b

ω0(b) = 0.11089

ω1(b) = 1.00000

ω2a(b) = 0.11089

ω2b(b) = 1.00000

359 G*

 

ω0(f) = 0.11089

ω1(f) = 1.00000

ω2a(f) = 999.00000

ω2b(f) = 999.00000

 
 

P0 = 0.20480

P1 = 0.56991

P2a = 0.05956

P2b = 0.16573

171 K**, 181 Q**,

Group 2c

ω0(b) = 0.06509

ω1(b) = 1.00000

ω2a(b) = 0.06509

ω2b(b) = 1.00000

192S**, 210 A**,

 

ω0(f) = 0.06509

ω1(f) = 1.00000

ω2a(f) = 5.55679

ω2b(f) = 5.55679

237 S**, 243 I**

 

P0 = 0.55167

P1 = 0.13832

P2a = 0.24786

P2b = 0.06215

25 N**, 26 I**, 34 C**, 79 S**,

Group 2d

ω0(b) = 0.08684

ω1(b) = 1.00000

ω2a(b) = 0.08684

ω2b(b) = 1.00000

148 T**, 208 G**, 214 D**,

 

ω0(f) = 0.08684

ω1(f) = 1.00000

ω2a(f) = 214.85997

ω2b(f) = 214.85997

269 H**, 363 C**, 395 N**

 

P0 = 0.27330

P1 = 0.60581

P2a = 0.03758

P2b = 0.08331

 

Group 2e

ω0(b) = 0.08686

ω1(b) = 1.00000

ω2a(b) = 0.08686

ω2b(b) = 1.00000

196 E*

 

ω0(f) = 0.08686

ω1(f) = 1.00000

ω2a(f) = 44.60691

ω2b(f) = 44.60691

 
 

P0 = 0.42970

P1 = 0.32076

P2a = 0.14288

P2b = 0.10666

 

Group 3

ω0(b) = 0.07702

ω1(b) = 1.00000

ω2a(b) = 0.07702

ω2b(b) = 1.00000

107 F*

 

ω0(f) = 0.07702

ω1(f) = 1.00000

ω2a(f) = 999.00000

ω2b(f) = 999.00000

 
  1. Note: *p < 0.05 and **p < 0.01 (x2 test).
  2. Site class: The sites in the sequence evolve according to the same process, the transition probability matrix is calculated only once for all sites for each branch.
  3. b: Background ω.
  4. f: Foreground ω.
  5. Positive delection sites: The number of amino acid sites estimated to have undergone positive selection.
  6. BEB: Bayes Empirical Bayes.
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BMC Genomics

ISSN: 1471-2164

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