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Meanwhile, back in the future, a modern-day sound program was used to visualize the wave pattern.
A Zeiss LSM710 confocal laser program was used to visualize co-localization between synphilin-1 and Alexa Fluor 488®conjugated CT-B.
Nimblegen's Signalmap program was used to visualize the DNA methylation data and for generation of profiling snapshots.
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The program Genesis [35] was used to visualize the relative expression profiles, to group related expression profiles with k-means clustering and to group tissues with hierarchical clustering.
The TreeView software program [ 106] was used to visualize the resulting phylogenies.
The program TreeView [ 95] was used to visualize the resulting trees.
Finally, the program VMD (Visual Molecular Dynamics) was used to visualize the model (Humphrey et al., 1996).
The program PyMOL (http://www.pymol.org/) was used to visualize and color structures as shown in Figure 2 and Figure 3.
The program WebLogo [ 7, 53]) was used to visualize the consensus for each USS.
The Swiss-PdbViewer program version 3.9b2 [ 85] was used to visualize the 3D structure and to highlight the relevant amino acid replacements identified in the evolutionary analyses.
The program Harvester (v.0.6.92; [ 94]) was used to visualize the Structure results and implement the Evanno et al. [ 37] ad hoc method, which detects the uppermost level of hierarchy.
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