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Authors' response : The toxin distributions in bacteria are certainly affected by lateral transfer so we cannot be certain of the inference of particular toxin in the common ancestor.
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However, such trees are just statistical inferences of particular historical events.
By this he means inferences from descriptions of particular instances of something to descriptions of that general kind of thing.
Moreover, the use of degenerated codons allow fast inference of trees, in particular with Maximum Likelihood (ML) methods which are faster with nucleotide sequences than with amino acid ones.
Without this, it is difficult to make reliable inferences of the absence of particular genes.
The Discussion should include how the missing treatment might affect your conclusions or further inferences about the role of particular volatile emissions.
At the same time, concerns have been voiced about the quality of inference: In particular, few studies have convincingly demonstrated that observed phenotypic shifts have a genetic basis (Gienapp et al. 2008; Merilä 2012).
The inference of diplotypes for a particular genotype is statistically a missing data problem that can be formulated by a finite mixture model.
Simulation studies show that the trimmed datasets returned by BMGE lead to inference of accurate trees, in particular when in presence of multiple alignments including distantly-related sequences.
Mitochondrial DNA primary sequences have also been extensively used for the inference of metazoan phylogeny, in particular in mammals and other deuterostome groups [ 28, 20, 16].
The RNAP largest subunit has played a key role in resolving such widely accepted hypotheses as the three domains of life [ 1, 2] and putative affiliation of the "long-branch" Microsporidia with fungi [ 3]; however, one particular inference of eukaryotic relationships based upon the RNAP II largest subunit (RPB1) has proven controversial.
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