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The objective of this work was to develop a comprehensive understanding of the operative rheology, processing conditions, cellular architecture, macrostructure and mechanical properties of high fiber, starch-based expanded matrices produced using extrusion.
In order to remove these possible sources of bias, a "background" RMSD was generated, averaging 10,000 RMSD matrices produced using DiA values generated from U and D values randomized across proteins (Figure 3B).
Comparisons between distance matrices produced using the gene-content methods were performed by calculating a sum-of-squares distance.
One-thousand bootstrap variations [ 64] of the alignment were generated using SEQBOOT and distance matrices produced using a structure-based scoring matrix [ 62, 63].
For example, the distance matrices produced using the four Thermococci (see table S3 for classification) as the conditioning genomes are clustered together.
One recurring feature of phylograms that are constructed from matrices produced using the CR approach is the presence of a few long branches in the analysis (see supplementary material).
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Figure 1c is a plot of the distances from a matrix produced using Methanosarcina acetivorans as the conditioning genome.
The degree of disagreement between the resultant MSAs can be assessed using a pairwise distance matrix produced using (e.g.,) MetAl distances (Blackburne and Whelan 2012).
Within our full dataset, all MRP matrices were produced using 'semi-rooted' MRP coding [ 37].
Geographic distance matrices were produced using the R package geosphere (Hijmans 2014).
Two final matrices were produced using the SHOT formulae in equations 1 and 2 above.
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