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MG1655 could not be completely assigned to the correct taxa.
Once an article has been identified, biocurators must properly specify the objects of annotation including confirmation of the correct taxa.
Overall, taxonomic assignments of taxator-tk were more rarely to false taxa at low ranks than with the other methods, and instead were to higher-ranking correct taxa.
The program TREENAMER (Leonard et al. 2009) was then run on the resulting tree files in order to restore the correct taxa names from the REFGEN tags used during phylogenetic processing.
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We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time.
Thus, it was not surprising that attendance during targeted, active-learning instruction on evolutionary relatedness was a significant predictor of correct taxa-relatedness reasoning.
If formal instruction is the most important factor for understanding phylogenetic trees, it should not be surprising that year in school and major were not correlated with correct taxa-relatedness reasoning.
They suggest that if Janko et al. [ 13] are correct, then asexual taxa with faster rates of clonal recruitment should be characterised by higher numbers of independent clonal origins and lower age estimates.
There is no expectation that this is the actual evolutionary history of these gene copies, or that it should provide the correct relationships among taxa, because multiple gene copies cannot all be orthologous to one another, and are homologous only at the level that there was one initial copy of 16S rRNA, but that is not informative at this phylogenetic level of inquiry.
This solution is preferable to correcting distances between taxa before constructing the phylogeny, because the construction of the phylogeny should incorporate variances due to coverage and sequencing error that would be removed by tip corrections.
Intron gain cases were inferred when the phylogenetic distribution of the intron was scarce or limited to a clade, given a correct sampling in related taxa or phyla (see paragraph Widely conserved introns and phylum-specific introns above).
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