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To focus our study on the most common conditions and sources of error, we removed all Mycoplasma and Candidatus sequences, as these taxa occur in very specific microbiomes and often have extremely fast-evolving sequences, which could present an additional source of inaccuracy.
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Notably, when analyzing such real biological data sets, additional sources of bias regarding MSA inaccuracies exist, for example, the inclusion of paralogs instead of orthologs, the inclusion of only partial sequences, or biases due to filtering of specific sequences and positions.
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(Margin of error takes into consideration only the size of a sample, which is usually the most trivial source of inaccuracy a pollster has to worry about).
Another source of inaccuracy is that we apply only two k-means iterations.
But no matter how much they tinker with these computer models, the companies can't do a thing about the most likely source of inaccuracy: the end user.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com