FigTree 1.2.1 http://tree.bio.ed.ac.uk/software/figtree/ was used for initial visualization and final production of figures of the resulting phylogenetic trees.
We used a 50-day local regression smoother (LOESS) for initial visualization of longer-term temporal patterns in the morbidity data (Cleveland and Devlin 1988).
The layout function "Edge-weighted Spring Embedded" was used for initial visualization of the clusters and the final maps were obtained by moving the nodes to prevent graphical overlap for better visualization.
Figure 8 shows an example of what this may look like for one region, but simply looking at different regions is inefficient, so we propose that the mitochondrial genome be used for initial visualization.
(C ) Five MCM models with lowest Rosetta energy of c-di-GMP riboswitch aptamer give an initial visualization of ligand-free ensemble (left); modeling included pseudo-energy constraints from 0 µM c-di-GMP and 10 mM Mg2+ proximity map.
As above, Rosetta modeling produced an initial visualization of a loose structural ensemble that samples, but does not stably remain in, the ligand-bound structure within the nanometer resolution of the MOHCA-seq method.
(C ) Five MCM models with lowest Rosetta energy of glycine riboswitch ligand-binding domain give an initial visualization of ligand-free ensemble (left); modeling included pseudo-energy constraints from 0 mM glycine and 10 mM Mg2+ proximity map.
(B ) Three MCM models with lowest Rosetta energy of AdoCbl riboswitch aptamer give an initial visualization of ligand-free ensemble (left); modeling included pseudo-energy constraints from 0 µM AdoCbl proximity map.
(Salmon et al., 2014, Bothe et al., 2011, Al-Hashimi, 2007)" "As above, Rosetta modeling produced an initial visualization of a loose structural ensemble that samples, but does not stably remain in, the ligand-bound structure within the nanometer resolution of the MOHCA-seq method".
(E ) Five MCM models with lowest Rosetta energy of glycine riboswitch ligand-binding domain without leader sequence give an initial visualization of ligand-free ensemble (left); modeling included pseudo-energy constraints from 0 mM glycine and 10 mM Mg2+ proximity map.
