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Ambiguity data were not removed from the data (cleandata = 0).
To resolve this ambiguity, data from several types of alignment media are used simultaneously during structure calculations.
For the analysis of mammal and fish alignments of complete sequences, sites with ambiguity data were removed (cleandata = 1) since they correspond to indels.
The codeml test implemented in PAML was used to compare five different nested models in two situations, i.e. including or excluding the ambiguity data in the alignment.
In order to determine the effect of alignment gaps, we also analyzed our sequences with the 66 alignment gaps included and treated them as ambiguity data [ 42, 43].
But for the analysis of the bird alignments, for which the sequences of some species were incompletely sequenced (see above), we did not remove sites with ambiguity data (cleandata = 0).
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The sequence composition and size of each amplicon were determined by Sanger sequencing (ABI 3130; Life Technologies, Burlington, Ontario) and compared with the filled gaps which in all cases show full agreement with no detectable ambiguities (data not shown).
9 11 31–37 All cases that demonstrate ambiguity in data definitions or outcome data will initially be discussed with site investigator; if ambiguity persists, the principal investigator and a locally convened panel of the research team will review, and consensus sought.
Though some solutions to current ambiguity in data usage and human rights may include a code of ethics, standards of operation, and a diversity in data, the discussion proved to be a catalyst for further discussions on human dignity, privacy, and ethics.
> -wrap-foot> Even where standard formats are adopted, the specifications themselves can result in ambiguity (Supplementary Data S1).
Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists.
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