PhyloD3

Expand the entire tree

You are about to expand the entire tree as provided by PhyloTree.

This operation is quite heavy and may require some time to complete.

Reset the tree

Proceeding will wipe all your work and reset the application at the initial state.

This operation cannot be reverted!

PhyloD3 Help

PhyloD3 allows to easily navigate through the human mtDNA phylogenetic tree as defined by PhyloTree.

PhyloD3 features:

Topology: obtained directly from PhyloTree, always updated to the latest version, just for you!
Easy Navigation: navigate among PhyloTree branches, freely zooming in and out to see the tiniest detail, as you do with yours best photos.
Easy Search: Search with confidence the haplogroup you need, helped by our autocompletion search bar. It will immediately appear with all its ancestors.
Custom detail: Take the lead! Open and close branches just by clicking on a haplogroup node: stop the flooding, only the right data, exactly where you need them!
Graphics that matters: In PhyloD3, graphics do matter. Collapsed haplogrups with subhaplogroups are filled in blue, white otherwise. Expanded haplogroups, instead, are always white colored.
Entire tree: Want to see the entire tree? Just click on the "Expand all" in the Options menu.
Reset: Played too much? Your tree is a mess? Reset everything to the initial state in one click thanks to "Reset" in the Options.

PhyloD3 is still in development, so various bugs may degrade your navigation. Our commitment is to iron them out as fast as we can!

PhyloD3 About

PhyloD3 is a concept realized by Dario Vianello, @Immunology Lab of the University of Bologna, to be presented at VIZBI conference in March 2014.

PhyloD3 stands for

Phylogeny with D3.js

Human phylogeny is obtained scraping PhyloTree, with the help of Python and BeautifulSoup library.

This Web Application is powered by:

D3.js: Visualization - Navigation - Ajax calls.
JQuery UI: Autocomplete module, to have a easier haplogroup search/selection.
JQuery: The glue that keeps everything together and make the whole thing work!
Twitter Bootstrap: Makes everything nice(r).
Heroku PaaS: Application hosting. By the way: give it a try! It's fabulous!

Additional features (e.g. display mutations) may come in the future, but we do not have a defined roadmap.

This website uses Google Analytics to track user behaviour.

These tracking information allows us to better understand how the users interact with PhyloD3 to improve it. No data able to uniquely indentify you is collected in this process.

PhyloD3 credits

Data shown in this application is provided by PhyloTree:

van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394.
http://www.phylotree.org
doi:10.1002/humu.20921

Many thanks also to Rob Schmuecker, who with this excellent blog post paved the way for the code that is now at the basis of PhyloD3.

Finally, a very big "Thank you all!!" to all our early testers, who helped us in improving this app.