P-values and position weight matrices were calculated using the Wilcoxon-Mann–Whitney test.
The components of stiffness and mass matrices were calculated using numerical integration of Gauss-Legendre.
Triangular similarity matrices were calculated using the Bray-Curtis similarity coefficient.
It should be noted that the score matrices were calculated between probes and galleries with the same quality values.
Raw intensity data were first normalized by square-root transformation and resemblance matrices were calculated using the Bray Curtis similarity coefficient.
Thirdly, resemblance matrices were calculated separately for each taxonomic group based on Bray-Curtis Similarity in Primer v6, and averaged in Microsoft® Excel (Figure 1).
For the results of the leaching experiments, correlation matrices were calculated utilizing Pearson's method to help identify possible relationships between the extracted concentrations, pH, time, and temperature.
Using those sampled complex structures as templates, energy matrices were calculated by running FoldX.
Protein distance matrices were calculated with PROTDIST using the PMB model [42].
The distance matrices were calculated by Tree-Puzzle (version 5.2) [5.2.
Community similarity matrices were calculated using a Bray-Curtis index on 4th root-transformed abundance data in order to reduce the contribution of common species [37].
