https://github.com/oseiskar/tree-of-life
Tree of Life visualization using d3.js
https://github.com/oseiskar/tree-of-life
d3 d3-visualization javascript visualization
Last synced: 2 months ago
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Tree of Life visualization using d3.js
- Host: GitHub
- URL: https://github.com/oseiskar/tree-of-life
- Owner: oseiskar
- License: other
- Created: 2015-10-03T14:54:08.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2019-06-15T10:25:08.000Z (almost 6 years ago)
- Last Synced: 2025-02-27T05:23:15.297Z (3 months ago)
- Topics: d3, d3-visualization, javascript, visualization
- Language: C++
- Homepage: http://oseiskar.github.io/tree-of-life/
- Size: 69.8 MB
- Stars: 7
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Tree of Life
This is an interactive visualization of the recently published
[Open Tree of Life](http://www.opentreeoflife.org/) using [d3.js](http://d3js.org/).
The entire tree with approximately 2.3 million identified species as leaf nodes
is browsable through the application. The width of the branches in the
visualization represents the number of species they contain.
The search feature can be used locate taxa in the tree by their scientific
(Latin) names such as _Canis lupus familiaris_, _Amanita muscaria_ or
_Streptococcaceae_.
### How it works
The original 80+ megabyte Newick tree file is split into many overlapping
subtress stored in JSON format. This operation is done with a C++ program
invoked with `make jsons`. The subtrees are lazily loaded when browsing
through the tree.
The program also constructs a prefix tree of the taxon names. This tree, which
powers the search feature, is also split into subrees that are loaded on demand.
All the resulting data can be hosted as static files, to create a "no-backend"
web application.
### Running locally
1. first download a suitable tree archive
[here](https://tree.opentreeoflife.org/about/synthesis-release/v10.3)
2. unpack and locate the `.tre` file with human-readable taxon names and
rename it `data/source.tre`
3. run `make jsons` (this requires `make` and `g++` installed on the system)
4. Run `python SimpleHTTPServer` and visi http://locahost:8000.
__See also [COPYRIGHT.md](COPYRIGHT.md)__