Other TreeViz Programs

Owned by Karen Cranston
Last updated: Mar 18, 2011Version comment
2 min read

Summary of tree viewers: Tree Viewers

Graph drawing libraries: Libraries

3D Graph/Tree layout algorithms: 3D Layouts

Information Visualization groups that have potentially useful projects: Research Groups

A wiki from the FMNH TreeViz working group that nicely summarizes some of the existing tools.

New tools from 2011 Vizbi conference:

A HTML and Javascript widget by Rod Page to embed a phylogeny in a web page: http://code.google.com/p/tvwidget/. Includes links to a set of blog posts about visualizing big trees

We should investigate algorithms for label layouts such as "Labeling with Leader" style algorithms that have focused on dense data labeling efforts http://www.springerlink.com/content/c8500130k854233u/. Nirav met Michael Kauffman who gave a talk at the UA CS dept and he gave some elegant/simple options on dealing with such issues. Karen had a similar conversation with Michael McGuffin (http://profs.logti.etsmtl.ca/mmcguffin/) who has some nice work on space efficiency in 2D layouts (http://profs.logti.etsmtl.ca/mmcguffin/research/#mcguffin_ivs2009).

We also might want to explore tree layouts that conform to geospatial data/layout  i.e constrain the tree for the phylo/bio geography type analysis/display . I have seen the population genetics folks try and use everything from Google earth and maps and integrate that with trees e.g http://panzea.org/db/searches/webform/geo_display_search. There is also a Mesquite module that will display a tree on Google Earth using the GPS coordinates for the specimens at the tips of the tree (http://mesquiteproject.org/packages/cartographer/googleEarth.html).

Biodiverse project looks interesting (spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix-based (e.g. genetic distance) relationships)

The Summon project is a python extension for any 2D visualization, providing an interface for OpenGL.

Some ideas for visualizing sets of trees:
Microbes online has a (very basic) gene tree viewer to view trees across the genome
TreeSetViz visualizes differences between hundreds or thousands of input trees using multi-dimensional scaling
DensiTree overlays many input trees
SplitsTree draws networks that describe sets of trees
TreeJuxtaposer excels at comparisons between small numbers of treees
GMap uses a map to see clusters in networks