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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.
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).
Similar(56)
Format ⑩ specifies how the dissimilarity matrix is exported (R-project, Phylip or tab-separated values).
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).
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.
In order to do this, the electron phonon coupling matrix and the Hamiltonian was exported out of gDFTB, transformed into an sp hybrid orbital basis and then orthogonalized.
Position data for the 30 min file was exported as a Matlab-compatable (Mathworks) matrix file.
Data was exported to Microsoft Excel to form a two dimensional matrix (ten samples versus seven variables) which was then exported to statistical (The Unscrambler X, CAMO, Trondheim, Norway) software for PCA and HCA anaysis.
STL was exported.
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