Table 3

Insertion/deletion rates among different phylogenetic groups estimated in rate variation model. Estimation was based on the common-genes trees.
Group
 Taxa
 Genome Size
 Branch Length
 Rate Variation
 Constant Rate
 ΔLnL






α value
 MLE
 LnL
 MLE
 LnL
Bacillus
 13
 4.9
 0.147413
 0.39
 3.89
 -40017
 0.44
 -40278
 261*
Brucella
 4
 2.1
 0.000275
 0.035
 382.06
 -1264
 44.50
 -1387
 123*
Burkholderia
 7
 3.8
 0.044985
 0.18
 181.93
 -17467
 2.14
 -18391
 924*
Candidatus
 4
 1.3
 0.433912
 ∞
 0.49
 -4722
 0.49
 -4722
 0
Chlamydophila
 7
 1.2
 0.096709
 0.39
 0.30
 -1439
 0.19
 -1466
 27*
Clostridium
 5
 3.3
 0.151053
 0.52
 8.49
 -9529
 7.23
 -9756
 227*
Corynebacterium
 5
 3.0
 0.223104
 1.19
 2.48
 -8492
 0.49
 -8509
 17*
Ehrlichia
 5
 1.5
 0.063546
 ∞
 0.24
 -831
 0.24
 -831
 0
Escherichia
 7
 5.0
 0.006966
 0.31
 13.43
 -10654
 4.82
 -11006
 352*
Helicobacter
 5
 1.7
 0.189516
 0.52
 1.75
 -3961
 1.05
 -4109
 148*
Lactobacillus
 6
 2.2
 0.331530
 ∞
 0.33
 -9241
 0.33
 -9241
 0
Mycobacterium
 6
 4.2
 0.087643
 0.23
 191.03
 -14660
 1.63
 -14718
 25*
Mycoplasma
 12
 0.9
 0.244815
 ∞
 0.22
 -8214
 0.22
 -8214
 0
Prochlorococcus
 5
 1.9
 0.319829
 2.56
 0.19
 -4413
 0.17
 -4419
 6*
Pseudomonas
 8
 6.3
 0.083078
 1.91
 1.06
 -26994
 0.91
 -27130
 136*
Rhodopseudomonas
 4
 5.3
 0.109002
 0.52
 1.75
 -9352
 0.77
 -9459
 107*
Rickettsia
 5
 1.3
 0.054524
 0.35
 3.49
 -3181
 1.36
 -3310
 129*
Salmonella
 5
 4.8
 0.003016
 0.080
 96.48
 -5214
 7.97
 -5351
 137*
Shigella
 6
 4.6
 0.004433
 0.17
 131.93
 -9784
 11.39
 -10327
 543*
Staphylococcus
 13
 2.8
 0.047252
 0.085
 279.41
 -11390
 14.76
 -14581
 3191*
Streptococcus
 19
 2.0
 0.053313
 0.29
 18.71
 -24327
 13.19
 -26553
 2226*
Synechococcus
 5
 2.6
 0.310236
 ∞
 0.33
 -7531
 0.33
 -7531
 0
Vibrio
 5
 3.2
 0.196671
 0.17
 10.02
 -8642
 0.37
 -8939
 260*
Xanthomonas
 6
 5.1
 0.026682
 0.59
 6.33
 -9385
 2.73
 -9541
 156*
Yersinia
 6
 4.6
 0.000355
 0.060
 221.14
 -3172
 31.15
 -3467
 295*

*Significant improvement

Hao and Golding BMC Genomics 2008 9:235   doi:10.1186/1471-2164-9-235