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Table 1 Sites of amino acid substitutions under positive selection computed by Mixed Effect model of evolution (MEME) analysis

From: Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

Gene Gene position α β q β+ P- value Log L KF041236 2010 2011 2013
Prm
  70£ 0 0 1.0 3916.54 .05 −8.79 S S A A
NS3
  10¥ 0 <.0001 1 278.84 .00 −11.26 P P P Y
NS4B
  130¥ 0 0 1 864.59 .04 −10.29 T T S T
NS5
  18¥ 0 0 .14 1888.34 .00 −11.51 N N S N
  440¥ <.0001 <0.0001 1.0 233.06 .09 −8.46     
  610¥ 0 0 1 38.47 .08 −8.05 N N G N
  1. ¥Amino acid substitution sites newly reported in this study.
  2. £Amino acid substitution already reported in Pakistan [14].
  3. α The maximum likelihood estimate (MLE) of the synonymous substitution rate α.
  4. β+ The MLE of the unconstrained β non-synonymous rate.
  5. βThe maximum likelihood estimate (MLE) of the non-synonymous rate for the branch class with β ≤ α.
  6. LRT -Likelihood ratio test statistic for β+ = α (null) versus β+ unrestricted (alternative).
  7. p- The p-value for the LRT test, using the mixture distribution: 0.33 χ2 0 + 0.30 χ2 1 + 0.37 χ2 2
  8. q- The q-value for independent tests (upper bound on the false discovery rate), derived from the corresponding p-value using Simes’ procedure.