By successfully replicating approximations of the NL and UK policies and their success, this research suggests that the PTTMAM could be used to focus on more specific policies and country conditions.
A GTR+I+gamma model of sequence evolution was used for the final maximum likelihood search, as suggested by the AIC in jModelTest 0.1.1 [ 51], while for rapid bootstrapping (103 replicates) CAT approximation of rate heterogeneity is implemented in RaxML [ 52].
The Shimodaira-Hasegawa, or SH, Test [ 84] was implemented in PAUP4b10 using 1000 replicates and RELL approximation.
Given that the technical replicates are an approximation, we set stringent NOISeq parameters to identify expression changes between treatments; i.e., high probability of differential expression (q > 0.99) and high normalized sequence counts difference between groups under comparison (>10,000).
A maximum likelihood analysis using RaxML v7.0.3 [42], [42] with 1000 bootstrap replicates under the GTRCAT approximation was run on the combined dataset to check for congruence with the Bayesian analysis.
Each of these alternate trees, which disrupt the evolutionary branching pattern of the major genotypes, was then tested against the optimal ML tree using Shimodaira's AU test with the RELL bootstrap approximation (1000 replicates), to determine if they were statistically inferior.
Our algorithm is based on a branching process approximation to replicating clones within a finite population.
ML analyses were conducted with RAxML v7.3.2 (Stamatakis et al. 2008) using the LG + G + F model of evolution and 1,000 fast bootstrap replicates based on CAT approximation.
Furthermore, our analysis is based on a limited number of replicates per model and parameter combination (100 replicate datasets), making our estimate of performance a Monte Carlo approximation given finite computational resources.
SH tests were implemented in PAUP, using the REEL approximation with 10,000 bootstrap replicates.
