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The aligned matrix was formatted for BEAST using BEAUti with the data partitioned to allow specification of DNA substitution models for each partition (see BI analysis above).
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The S matrix is formatted with rows as metabolites and columns as reactions.
Each expression matrix is formatted as in Figure 3A, and each module assignment matrix as in Figure 4B F.
The CDD position specific scoring matrix (PSSM) for Mab-21 domain was formatted as database using the formatrpsdb program (BLAST utility in the BLAST suite) and parameters set as described in ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/README file.
The data used for the analysis was formatted to create a balanced design matrix.
The data from the evidence matrix will be formatted to create a visual representation which facilitates interpretation.
Multiply normalized total criteria relation matrix T c * with normalized total dimensions relation matrix T d * to produce the originally weighted super-matrix S, which is formatted in Eq. (11).
The S is further transposed to a column-stochastic super-matrix S *, which is formatted in Eq. (12).
The call data and organizational structure were formatted into UCINET matrices and analyses were run using both UCINET and NetDraw (the visualization software).
Alternatively to the HTML format, analysis results can be formatted in a tab-delimitated matrix into a simple text file.
The matrix was the only format with which all of the provided information was visible at once, on a single sheet of paper.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com