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Figure 2 shows the schematised majority rule consensus NJ jackknife tree and Figure 3 shows the schematised majority rule consensus MP jackknife tree of the condensed dataset.
This condensed dataset consisted of 916 genotypes.
The condensed dataset was used in both phenetic and cladistic analyses and in the resampling methods.
For further analysis a condensed dataset was created by carefully choosing a representative genotype from all the available accessions.
A condensed dataset was created by choosing a representative genotype from all the available accessions (see methods section for exact details).
Besides choosing only one genotype per accession to represent the accession in the condensed dataset, other adjustments were made to create this dataset.
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Finally, to obtain a condensed input dataset for the BEAST analyses (see below), we built a combined plastid and ITS matrix with multiple accessions per species merged into a single consensus sequence using the "merge sequence" function in MacClade 4.08 [ 68], which resulted in 262 ingroup taxa (6274 nucleotides, 1% gaps, 65% missing data).
In Figure 7, this large dataset is condensed and re-inferred to include sequences from a limited number of bacterial and cyanobacterial representatives; rhodophytic as well as CASH plastids.
These 2 datasets were condensed to 82,872 terms for 12,133 transcripts after accounting for redundancy between datasets.
This approach was able to condense the enormous dataset to a manageable subset of discriminative genes, which can now be subjected to detailed functional studies.
The paper is aimed at detecting the main factors determining the composition of Central European village floras and their ecological uniqueness by exploitation of the condensed ecological information of quasi-complete datasets of their spontaneous (and subspontaneous) vascular plants.
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