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TEs that overlapped in these alignment files were discarded to avoid ambiguities in the inference of substitution rates.
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Poorly aligned positions in these alignments were removed, with only the conserved region the CDK domain for the CDK family, and Cyclin-N and –C domains for the cyclin family—used for further phylogenetic analyses.
But the settlement that is implicit in these alignments is not possible if Mr. Clinton continues to demand that we, as a people, endorse his lying.
To test for mutational saturation in these alignments we constructed NJ trees considering all substitution sites and then solely the unsaturated fraction of sites using ASATURA [16].
Closer inspection of the repeats in these alignments which did not conform revealed them to be either obvious misalignments or apparent false positives.
In contrast to some previous studies [20], [21], we observed a negative correlation with the number of sequences in these alignments, i.e. the alignments with a larger number of sequences were less well aligned.
We find that the seven and five most significant eigenpositions and corresponding eigenorganisms uncovered in the 16S and 23S alignments, respectively, capture <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0018768.e020.PNG" class= inline-graphic"/> 88% and 87% of the nucleotide frequency information in these alignments (Figures S1 and S2 in Appendix S1).
The remained regions in these alignments were also concatenated.
The top 19 species in these alignments are diptera.
The information gathered in these alignments is stored in the database.
This phenomenon was particularly evident because sequences from distant Anthozoa representatives were included in these alignments.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com