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Artemis comparison tool (ACT; Carver et al., 2005) and Mauve (Darling et al., 2010) are both examples of excellent comparative genome analysis tools that are widely used to generate figures for publication, but are not designed for this purpose and generally lose clarity when displaying several regions at once.
IPA also was used to generate figures for network interaction of gene sets for ncRNAs.
# First: setup global configuration > PKconfig general.list, hist.list, scatter.list) #Second: match metric system > PKdata data=pdata, match.term=var.name) The main goal of this step is to generate figures for model diagnostics.
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Forest plots in excel software were used to generate figures (1a – c) for multivariate analysis [10].
We used the R code of Drummond et al. (2006) to generate figures and tables for principal component regression.
These values were used to generate Figure 3. Furthermore, for each pair of strains, a pairwise distance was computed representing the proportion of genome content that they have in common.
Additional file 5: Data used to generate Figure 3 A. Data 5 1: Data for calculation of CIs for kinase groups.
Data from the DNA microarray hybridizations and the in silico hybridizations were compiled to generate Figure 6 using Spotfire (Somerville MA) for data visualization.
This file contains a Cytoscape 3 session file (*.cys) containing five networks used to generate Figure 3– Figure 5. Click here for additional data file.
Finally, BIGDAWG generates figures and tables for each of these comparisons.
MT conducted bioinformatic analyses on EST sequences, performed manual and automatic gene model curation, coordinated Genbank submissions, and generated figures and tables for the manuscript.
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