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As in [10], we adopt a Bayesian approach to the data fitting, implemented by a variational Bayes approach.
The iterative fitting implemented in the RMSDTT plugin performs a by-residue weighted pairwise fitting, such that after each iteration, residues with lower average RMSD are assigned higher weights in the next iteration.
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The landmark coordinates for the different data subsets were processed with the Procrustes fit implemented in MorphoJ [ 60].
Average optical constants were determined for both types of gold surfaces (B-spline material fit implemented in the measurement software CompleteEASE).
The MXCOMP subroutine was used to calculate a cophenetic correlation matrix between the genetic similarity matrix and the tree matrix to measure goodness-of-fit implemented in the NTSYSpc package.
Differential expression analysis between wild-type and Ddit3−/− Pmel CD8+ T cells was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
For each phylogroup, the occurrence of recent spatial expansions (assuming constant deme size) was tested with ARLEQUIN 3.1 [ 98], fitting the implemented model to the observed mismatch distribution.
We also visualized genomic differentiation by a sliding window approach using local polynomial fitting (LOESS) implemented in R (R Development Core Team [ 34]; 2nd order polynomial with band width of 0.4; using simpler polynomials and different band widths did not alter our conclusions).
So a rigid alignment was applied to superimpose d-5 compounds onto an unsubstituented template shown in Figure 2 using an atom-by-atom least-squares fit as implemented in the SYBYL FIT option, and compound d-5 with the best biological activity was treated as the reference molecule.
The non-linear least squares fit function implemented by Bates and DebRoy into the "nls" packet of R was used for the sine fit.
The amino acid substitution model was chosen using best maximum-likelihood fits as implemented in MEGA5 [ 94].
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