Resolution:
## Figure 3.
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 |