Web-based

• Suggested by Paul Thomas, we can use iTOL. Seems to have API.

• This is a javascript SVG based visualization tool jsPhyloSVG. Seems to have API, and moreover, suitable to be used with Shiny. Elsevier uses this. So far, this is the tool that I like the most.

• SILVA Tree Viewer is a webapp.

• TreeLink is a webapp.

• PhyD3 makes interactive visualizations. Suitable for Shiny.

In R

• The ape::plot.phylo function has several options that I was not aware of. Now that I realized that the coordinates of the nodes are stored in .PlotPhyloEnv$last_plot.phylo as xx and yy, I can use this as input to create more personalized visualizations.

• The ggtree R package, currently used here, is not working properly when handling the annotations.