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Binned matrices were exported from the program for parsimony phylogenetic analysis by PAUP (not a recommendation of the program's creators) or were used to calculate a pairwise distance matrix using the CGHdist method implemented in MPP.
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These partial sequences were trimmed and aligned using the RDPII pipeline tools [50] and a distance matrix was exported to DOTUR [51] for dereplication of each library.
Format ⑩ specifies how the dissimilarity matrix is exported (R-project, Phylip or tab-separated values).
The resulting binary matrix was exported in the form of comma-separated text for data analysis.
Also, one distance matrix was exported from Gegenees in the "nexus" format for use as the input into SplitsTree4.
The matrix was exported in nexus format and analysed using the default pipeline in SplitsTree 4 (as above).
The data-matrix was exported as a nexus file into PAUP 4.0 (Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).
Strain curves were exported as digital matrix data to a proprietary, open source analysis software (StrATo version 2.0.3.0).
The results were exported as presence/absence matrix.
Processed data were exported as a presence/absence matrix.
Scored results were exported to an Excel matrix with values 1 (allele present) or 0 (allele absent).
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