This is an open problem in information visualization. Lots of work has been done but it doesn’t seem like anything completely general and satisfying has been hit upon. In the infographics sphere, it seems that more effort is being put into showing really huge trees as a way to blow people’s minds, so clarity hasn’t been a concern. In the stats world, it’s been about reducing what needs to be drawn, e.g., through clustering.
Lit Review, Blogs, etc.
Citation Networks
CiteGraph: a citation network system for MEDLINE articles and analysis.
https://www.ncbi.nlm.nih.gov/pubmed/23920674
Modelling the Footprints of Innovation: Citation Networks (blog entry)
CitNetExplorer
Miscellaneous Networks
PhenoBlocks: Phenotype Comparison Visualizations. Glueck, Hamilton, Vis2015
Vials: Visualizing Alternative Splicing of Genes. Borowosky, Pfister, Lex, Vis2015
A novel method for large tree visualization. Jeff Heard, William Kaufmann, Xiaojun Guan
http://bioinformatics.oxfordjournals.org/content/25/4/557.long
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642634/
seems to be a circle layout where dense branching is turned into wedges/triangles?
A space-optimized tree visualization. Quang Vinh Nguyen, Mao Lin Huang
http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=1173152
Hierarchical Edge Bundles. Danny Holten. 2006
http://www.aviz.fr/wiki/uploads/Teaching2014/bundles_infovis.pdf
d3.js examples on hierarchical edge bundling:
http://bl.ocks.org/mbostock/4341134
https://bl.ocks.org/mbostock/7607999
tulip - no longer supported?
http://tulip.labri.fr/TulipDrupal/
Stackoverflow-style discussion at Biostars
https://www.biostars.org/p/2438/
Dendroscope
Walrus
https://www.caida.org/tools/visualization/walrus/
ETE Toolkit (python lib)
http://etetoolkit.org/gallery/
http://etetoolkit.org/docs/latest/tutorial/tutorial_clustering.html
NetworkX
Edge contraction
https://en.wikipedia.org/wiki/Edge_contraction
Blog about simplifying a network graph http://blog.revolutionanalytics.com/2015/08/contracting-and-simplifying-a-network-graph.html