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Multiple nucleotide sequence alignment of gene was calculated and presented by using the DNAMAN program.
Multiple nucleotide sequence alignments were performed separately on the eight viral gene segments of representative viruses using Clustal W (BioEdit version 7.0.5) (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
The strategy of this algorithm was designed to carefully select a set of common PCR primer pairs from the conserved regions by multiple nucleotide sequence alignment.
Multiple nucleotide sequence alignments were performed using all available R. irregularis mitochondrial genomes published so far.
The multiple nucleotide sequence alignment was performed using the ClustalW algorithm implemented in MEGA5.2 software [ 29].
Multiple nucleotide sequence alignments of isotigs identified among the EST libraries were undertaken to identify putative SNPs.
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Multiple nucleotide sequences were performed with the ClustalW2 program http://www.ebi.ac.uk/Tools/clustalw2/index.html.html
The Motif Sampler [ 28, 29] tool allows users to predict common conserved motifs for multiple nucleotide sequences and rank them according to the scores.
Multiple nucleotide sequences were aligned in both the 5′ and 3′ directions for each positive tick pool or isolate using SeqMan software (DNASTAR).
Using these methods, multiple nucleotide sequences were generated for each positive tick pool, as well as for the isolates derived from these pools.
One approach for deriving meaningful information on population genetics is by comparing multiple nucleotide sequences, including arbitrary regions [ 19], and subsequent assessment of calculated patterns of diversity, tests of selection (Tajima's D, Fu and Li's F* and D* statistics), gene flow, linkage disequilibrium and migration [ 20].
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