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The matrix was imported into Excel 2007 (Microsoft Corporation, Redmond, WA, USA), and conditional formatting was used to identify relationships between sequences in the ranges 95%100%and90% 94.9%.95%100%and90% 94.9%
The proton nuclear magnetic resonance (1H NMR) spectra were reduced to ASCII files using OACD software; the resulting data matrix was imported into The Unscrambler 10.1 software (www.camo.com).
The rank matrix was imported in Cytoscape to construct the network of co-expressed genes.
The distance matrix was imported into DOTUR [26] to cluster the RDP sequences into phylotypes (OTUs) of maximum within-cluster dissimilarity (furthest neighbor) of 3%.
The matrix was imported into Phylip v3.67 [ 55] for the construction of the neighbor-joining tree.
The final data set (X matrix) was imported into the SIMCA-P+ program (Version 13.0, Umetrics, Sweden), mean-centered and Pareto scaled column wise.
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These 100 matrices were imported into the FastME program to obtain 100 inversion and breakpoint distance-based trees.
Prior to analysis, the AMOVA matrices of genetic distance were generated in Arlequin 3.1, the square root of each distance was taken, and the matrices were imported to PERMANOVA+.
Dissimilarity matrices were imported into the R environment (39) and analysed by multiple clustering algorithms.
FST matrices were imported into paup* (Swofford 2002) to estimate a neighbor-joining (NJ) tree to visualize the degree of separation of the populations.
The matrix of genetic distances was imported in GenAlex ver. 6.4 (Peakall and Smouse 2006) and analysed in a principal coordinate analysis (PCoA).
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