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The clustering analysis divided Group II C. botulinum into three main clades using a distance marker of 0.5.
Type I pili have previously been categorized into 3 main clades using a global pneumococcal collection (12).
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Patterns of nucleotide diversity within each species and for each main clade identified using the phylogenetic analysis are summarized in Table 1.
The divergence times of the main clades within the Annonaceae (derived here using BEAST) deviate slightly from those previously determined using different calibration points and dating methods.
The average p distances between the main clades were also calculated for both markers using the program MEGA v.3.1 [ 80].
In comparison to the phylogenetic analysis using dataset 1, the position of the main clades within Musaceae in dataset 2 remained conserved in BI tree.
The existence of potential haplotype sharing between main clades revealed by phylogenetic analyses was investigated for each marker using Arlequin 3.11 [ 47].
A phylogenetic tree of 280 concatenated protein sequences was constructed using this methodology and produced a tree with 11 main clades with higher than 80% bootstrap support.
A pilot study, designed to quantify the incorporation of phytoplankton-derived carbon by the main clades of heterotrophic aquatic bacteria (i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes), is used to exemplify and suggest potential solutions to these technical difficulties.
Analysis of phylogenetic tree by using 16S rDNA sequences had led to the formation of three main clades, including Streptomyces, Pseudonocardia, and Nocardiopsis.
The divergence times of the main clades within the Annonaceae were found to deviate slightly from previous estimates that used different calibration points and dating methods.
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