CNV variant plots imposted on local trees
figureposted on 16.09.2016 by Daniel Jeffares, Liam Shaw, Fritz Sedlazeck
Figures are generally photos, graphs and static images that would be represented in traditional pdf publications.
CNV variant plots imposted on local trees, as shown in Figure 3 of the manuscript.
For each CNV we extracted all SNPs from 20 kb upstream and 20 kb downstream. We then used these concatenated SNPs to build a local SNP-based tree with FastTree. The copy numbers of each strain were imposed on this tree.