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. 2011 Oct 6;12:487. doi: 10.1186/1471-2164-12-487

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Copyright ©2011 Gilbert et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Results for MPP based NJ and Parsimony Analysis. The stacked histograms show the SymD measures of trees constructed using the MPP method for the sixteen different iterations detailed in Additional File 1: table S1 - representing the various options available in the MPP program. The binary matrices constructed by MPP were output to PAUP and used to make parsimony-based trees (Figures 4 C and D). From each binary matrix a distance matrix was calculated from each of these sixteen matrices using the cghdist option in the MPP GUI, and a Neighbor-Joining (NJ) tree was calculated using PAUP excluding (Figure 4A) and including (Figure 4B) the reference taxon, N. crassa A. This data is also given table form in Additional File 4: table S4.