Results for NJ and Parsimony analysis of Relative Bayesian Estimated Hybridization Levels. Figure 3 show the stacked histograms of the SymD measures for Neighbor-Joining tree construction of the ACUITY and Limma-based normalizations processed with the BAGEL program. Five trees are represented in each stack, constructed from each of the four normalizations done and the additional linear normalization based on the ratio of the medians (see Additional File 1: table S1). Only these five datasets were input into BAGEL as it only accepts log-transformed data. Figures 3A and 3B show the results for the NJ algorithm excluding and including N. crassa A respectively for the symmetric distance. Figures 3C and 3D show the SymD measures from parsimony analysis of the BAGEL-estimated values converted to binary matrices as described in the methods. The same data is given in table form in Additional File 3: table S3.
Gilbert et al. BMC Genomics 2011 12:487 doi:10.1186/1471-2164-12-487