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We again considered a dominant, a recessive, an additive "per-allele" model and pairwise comparisons.
Poisson correction amino acid model and pairwise deletion of gaps were selected for the tree reconstruction.
The unrooted tree was constructed using MEGA 5 [ 71] with the neighbour-joining method and 1,000 bootstraps (Poisson model and pairwise deletion).
DOI: http://dx.doi.org/10.7554/eLife.06134.012 10.7554/eLiFigure34.013 Figure 5 figure supplement 3. Comparing response similarity derived from the conditionally independent model and pairwise model.
We then built neighbor-joining (NJ) tree for each gene region using Kimura 2-parameter (K2P) distance model and pairwise deletion in MEGA 4.0.
Tumour weight was analysed with an ANOVA model, and pairwise comparisons among the four treatment groups were made using Tukey's studentised range test (HSD) (Christensen, 2002).
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Experimental groups were compared with control groups using the general linear model (GLM) and pairwise t-tests for equal or unequal variances.
The approach is demonstrated in a plug-flow reactor (PFR) model and a pairwise mixing stirred reactor (PMSR) model.
Finally, the methodology is demonstrated using n-pentane combustion in an adiabatic plug flow reactor model and a pairwise mixing stirred reactor model.
The core of the method is based on a wavelet-domain hidden Markov tree model and a pairwise classifiers design and selection.
Thus, the explicit stochastic network simulation model and the pairwise model combine favourably to provide a more accurate model with some degree of analytical tractability.
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