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All reconstructed datasets were analysed using VivoQuant software (v2.0, inviCRO, LLC, Boston, USA).
Where appropriate, differences between datasets were analysed using a two-tailed paired Students T test.
Datasets were analysed using FlowJo.
Datasets were analysed using descriptive statistics.
Both datasets were analysed using the program MrBayes (see below).
All three datasets were analysed using the same MP settings.
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Each of the simulated datasets was analysed using the four approaches described above.
These 'completed datasets' are analysed using the appropriate statistical model for the epidemiological analysis and the estimates obtained from each dataset are averaged to produce one overall MI estimate.
Three data sets (the full data set and two sub-datasets) were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial.
For this purpose, sequences that had been classified as false positives in the synthetic dataset and uniquely classified in the experimental metagenome dataset were analysed using MEGABLAST.
The same dataset was analysed using Mx (Neale 2004).
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