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In any cluster analysis, the matrixes were built up according to co-citation or -occurrence times between the selected articles or words.
Homologues of the PhoP box identified from the PhoP sites were then collected and displayed by the WebLogo program [ 23] to generate a sequence logo; additionally, the position count matrixes were built from them by using the consensus-matrix and convert-matrix tools [ 21].
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GMMs with diagonal covariance matrix were built for every category while testing consisted of a simple comparison of log-likelihoods.
For the 3DZD, similarity matrices were built based on the three different measures of the correlation coefficient (r), DE, and DM.
Binding matrices were built using the standard Delila programs [19], [20].
Phylogenetic analyses and distance matrices were built using the Mega5 package [ 19].
Another two IBD matrices were built up for two different genotyping structures: moderate and extensive gaps.
Migration matrices were built describing numbers of connections between 27 subtype H3N2 or 29 subtype H1N1 predefined geographic regions.
The networks for Γ f matrices were built with the same contact/noncontact filtering applied to the I LL n matrix (see preceding section).
Meanwhile, binary adjacency matrices were built for each subject by applying three different cut-off values (0.1, 0.15 and 0.25) to the correlation matrix.
The alternative matrices were built using genes first identified in ACURs (Alternative Codon Usage Regions) based on homology and taken from the R. solanacearum annotation process [ 47].
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CEO of Professional Science Editing for Scientists @ prosciediting.com