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For each dataset, analysis was carried-out using an interface developed at the University of Lausanne (Gene Expression Data Analysis Interface (GEDAI)) [ 38].
Results were similar for the complete dataset analysis and the imputed dataset analysis.
These parsimony analyses were performed following the same protocol and methods described for the full dataset analysis listed above.
Availability: The intuitive interface for dataset exploration, analysis and prediction is available at http://s.tartaglialab.com/clever_suite.tartaglialab.com/clever_suite
However, only a limited number of bioinformatics tools are available for ChIP datasets analysis.
For other datasets, analysis to the appropriate local level may not be conducted routinely.
Declarations of suggestive or significant QTL were made separately for each dataset and analysis method.
For this dataset, parsimony analysis shows a length of 27412 steps, with CI =0.313, RI = 0.499.
This gave us 183 datasets per outbreak per baseline, for a total of 226,920 datasets for analysis.
The data were entered into a Progeny database (Progeny Software, LLC, South Bend, IN) for the generation of datasets for analysis.
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