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. 2019 Jan 14;19:22. doi: 10.1186/s12862-018-1326-7

Table 6.

Results of applying LRT-1 and LRT-3 to the set of 21 real Streptococcus sequence alignments

Gene under-fit models over-fit models M2a vs. G2a13
NC NS TL LRT-1:
M1a vs. M2a		 M2a
MLEs		 LRT-3:
G1a13 vs. G2a13 		G2a13
MLEs		 2Δl
1 892 19 6.98 N.S. ω+ = 1.0
p+ = 0.026		 N.S. ω+ = 1.02
p+ = 0		 881.3
2 639 16 6.37 N.S. ω+ = 1.0
p+ = 0.15		 P < 0.0001 ω+ = 4.9
p+ = 0.028		 504.2
3 228 11 3.74 N.S. ω+ = 1.0
p+ = 0.046		 N.S. ω+ = 1.2
p+ = 0		 152.1
4 577 9 8.49 N.S. ω+ = 1.0
p+ = 0.05		 N.S. ω+ = 1.18
p+ = 0		 466.1
5 390 9 5.16 N.S. ω+ = 1.0
p+ = 0.19		 P < 0.0001 ω+ = 11.7
p+ = 0.03		 109.6
6 348 11 4.5 N.S. ω+ = 1.0
p+ = 0.04		 N.S. ω+ = 3.11
p+ = 0		 113.7
7 184 10 0.37 P < 0.0001 ω+ = 5.29
p+ = 0.24		 P < 0.0001 ω+ = 4.36
p+ = 0.29		 71.7
8 169 6 30 N.S. ω+ = 1.0
p+ = 0.001		 N.S. ω+ = 8.46
p+ = 0.02		 130.9
9 227 10 5.46 N.S. ω+ = 1.0
p+ = 0.25		 N.S. ω+ = 20.5
p+ = 0.14		 50.3
10†§ 450 10 2.2 N.S. ω+ = 1.0
p+ = 0.06		 N.S. ω+ = 1
p+ = 0		 14.3
11 444 7 4.6 N.S. ω+ = 1.0
p+ = 0.31		 N.S. ω+ = 1.03
p+ = 0		 109.7
12 473 9 0.45 N.S. ω+ = 1.0
p+ = 0.21		 N.S. ω+ = 10.6
p+ = 0.007		 17.3
13 427 8 0.05 0.10 > P > 0.05 ω+ = 15.7
p+ = 0.006		 N.S. ω+ > 99
p+ = 0.02		 6.2
14 632 7 0.09 0.10 > P > 0.05 ω+ = 15.3
p+ = 0.016		 N.S. ω+ = 22.5
p+ = 0.03		 25.1
15† 209 7 10.3 N.S. ω+ = 1.0
p+ = 0.05		 N.S. ω+ = 1
p+ = 0		 164.5
16 232 6 0.43 0.10 > P > 0.05 ω+ = 9.4
p+ = 0.29		 N.S. ω+ = 2.3
p+ = 0.37		 49.1
17 661 5 3.3 N.S. ω+ = 1.0
p+ = 0.27		 P = 0.051 ω+ = 1.0
p+ = 0.33		 220.6
18 564 5 7.7 N.S. ω+ = 1.0
p+ = 0.5		 N.S. ω+ = 1.3
p+ = 0		 171.4
19 261 4 9.5 N.S. ω+ = 1.0
p+ = 0.04		 N.S. ω+ = 1.0
p+ = 0		 113.6
20 201 4 2.2 N.S. ω+ = 1.0
p+ = 0.03		 N.S. ω+ = 17.8
p+ = 0.04		 40.4
21† 166 4 2.7 N.S. ω+ = 2.15
p+ = 0.20		 N.S. ω+ = 17.8
p+ = 0.017		 34.69

NC is the number of codons in the sequence alignment after removal of sites with ambiguities or indels. NS is the number of gene sequences in the alignment. TL is the total tree length estimated under codon model M0 as the mean number of substitution per codon. N.S. indicates a non-significant LRT. The dagger symbol (†) indicates a gene for which likelihood optimization under a G-series model did meet convergence criteria. The two-fold s symbol (§) indicates that the MLEs were obtained by removing tip branches having near-zero lengths and re-fitting the model. The gene names, along with the sequence alignments, are provided in the DRYAD repository [51]