We assumed the 4by4 nucleotide model, mixed number of substitution types and gamma-distributed substitution rates with five categories.
Tree reconstruction option, uses user defined tree search procedure, clocklike branch lengths on, exact parameter estimates, "JTT" substitution model, mixed model of rate heterogeneity (1 invariable + 8 gamma rates).
A generalized linear mixed model with gamma distribution for repeated measures, adjusted for rejection, recipient/donor age and delayed graft function, was used for statistical analysis.
For comparison of levels of hsTnT and NTproBNP over time between patients with poor and good outcome, a generalised linear mixed model with gamma regression was used due to non-normal distribution of hsTnT and NTproBNP.
For Bayesian analysis, a mixed substitution model with gamma law (four rate categories) and a proportion of invariant sites were used.
Bayesian phylogenetic analyses were conducted with MrBayes 3.1.2 [28] using a mixed amino acid model with gamma, which selected RtRev with a 100% posterior probability with 3,000,000 generations sampled every 100 generations with 4 chains over 4 independent runs.
Bayesian phylogenies were generated in Geneious with Mr. Bayes [ 47] using the mixed amino acid model with gamma distributed variation rates, a uniform branch length clock, and MCMC settings of 4 heated chains for 1000000 generations.
