https://github.com/cmzmasek/archaeopteryx-js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
https://github.com/cmzmasek/archaeopteryx-js
analysis archaeopteryx archaeopteryx-js evolution javascript phylogenetic-trees phylogenetics visualization
Last synced: 25 days ago
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Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
- Host: GitHub
- URL: https://github.com/cmzmasek/archaeopteryx-js
- Owner: cmzmasek
- License: lgpl-2.1
- Created: 2016-09-09T21:49:39.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2026-02-24T00:45:43.000Z (4 months ago)
- Last Synced: 2026-02-24T07:32:14.999Z (4 months ago)
- Topics: analysis, archaeopteryx, archaeopteryx-js, evolution, javascript, phylogenetic-trees, phylogenetics, visualization
- Language: JavaScript
- Homepage: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js
- Size: 7.49 MB
- Stars: 41
- Watchers: 6
- Forks: 15
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Archaeopteryx.js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
### Website
https://sites.google.com/view/archaeopteryxjs
### npm
https://www.npmjs.com/package/archaeopteryx
### GitHub
https://github.com/cmzmasek/archaeopteryx-js
### Examples
* [Bcl-2 gene family](http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html)
* Eukaryotic tree of life:
* [collapsed with initial depth = 5](http://www.phyloxml.org/archaeopteryx-js/euk_tol_collapsed_js.html)
* [uncollapsed](http://www.phyloxml.org/archaeopteryx-js/euk_tol_js.html)
* [Influenza HA H3 collapsed by Country](http://www.phyloxml.org/archaeopteryx-js/influenza_collapsed.html)
* [Amphibian phylogeny](http://www.phyloxml.org/archaeopteryx-js/amphi_frost_js.html)
* Visualizations:
* [Herpesviridae DNA polymerases](http://www.phyloxml.org/archaeopteryx-js/hg1001_js.html)
* RAxML examples:
* [bipartitions](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_bcl2_js.html)
* [bipartitionsBranchLabels](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_branchlabels_bcl2_js.html)
* MSA Residue Visualization:
* [Bunyaviridae Glycoprotein](http://www.phyloxml.org/archaeopteryx-js/bunya_glycoprotein.html)
* [Bcl-2 protein](http://www.phyloxml.org/archaeopteryx-js/bcl2_msa.html)
* Preset search fields:
* [H3N2](http://www.phyloxml.org/archaeopteryx-js/h3n2_search_js.html)
* Grouping of species and years for visualization:
* [Viral Strains](http://www.phyloxml.org/archaeopteryx-js/many_species_js.html)
* SARS-CoV-2 with mutations and PANGO lineages:
* [SARS-CoV-2](http://www.phyloxml.org/archaeopteryx-js/sars_cov_3.html)
### Detailed developer documentation
https://docs.google.com/document/d/1COVe0iYbKtcBQxGTP4_zuimpk2FH9iusOVOgd5xCJ3A/edit
### Version History
https://github.com/cmzmasek/archaeopteryx-js/wiki/Archaeopteryx.js-Version-History
### Dependencies
Archaeopteryx.js has the following dependencies:
* forester.js: https://www.npmjs.com/package/archaeopteryx
* phyloxml.js: https://www.npmjs.com/package/phyloxml
* d3.js (version 3): https://www.npmjs.com/package/d3/v/3.5.17
* jQuery (1.12.4): https://www.npmjs.com/package/jquery/v/1.12.4
* jQuery UI (1.12.1): https://www.npmjs.com/package/jquery-ui/v/1.12.1
* sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4
For file (Newick/New Hampshire, phyloXML) and graphics (PNG, SVG)
download/export, the following five libraries are required as well:
* canvg: https://www.npmjs.com/package/canvg
* rgbcolor: https://www.npmjs.com/package/rgbcolor
* Blob.js: https://github.com/eligrey/Blob.js
* canvas-toBlob.js (needed in some versions of Internet Explorer and Opera): https://github.com/eligrey/canvas-toBlob.js
* FileSaver.js: https://github.com/eligrey/FileSaver.js
Additionally, Archaeopteryx.js also requires the following CSS:
* jquery-ui.css: https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css
## Basic Example of HTML for launching Archaeopteryx.js
Example of HTML page to launch a basic Archaeopteryx.js instance:
```
Archaeopteryx.js Basic Demo
function load() {
var options = {};
options.backgroundColorDefault = '#f0f0f0';
var settings = {};
var loc = 'https://raw.githubusercontent.com/cmzmasek/archaeopteryx-js/master/test/data/phyloxml_trees/apaf.xml';
jQuery.get(loc,
function (data) {
var tree = null;
try {
tree = archaeopteryx.parseTree(loc, data, true, false);
}
catch (e) {
alert("error while parsing tree: " + e);
}
if (tree) {
try {
archaeopteryx.launch('#phylogram1', tree, options, settings);
}
catch (e) {
alert("error while launching archaeopteryx: " + e);
}
}
},
"text")
.fail(function () {
alert("error: failed to read tree(s) from \"" + loc + "\"");
}
);
}
Archaeopteryx.js Basic Demo
```
# forester.js
forester.js is a general suite for dealing with phylogenetic trees.
## forester.js Example
This basic example shows how to parse a New Hampshire formatted String
into to a object representing a phylogenetic tree.
Followed by pre- and post-order traversal,
and writing back to a New Hampshire formatted String.
Change './forester' to 'forester' if you use this code outside of this package
```
var forester = require('./forester').forester;
var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
console.log('Pre-order traversal:');
forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
console.log(n.name + ':' + n.branch_length);
});
console.log('Post-order traversal:');
forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
console.log(n.name + ':' + n.branch_length);
});
console.log('In New Hampshire format:');
var nh = forester.toNewHampshire(phylogeneticTree);
console.log(nh);
```
Expected output:
```
Pre-order traversal:
R:1
f:1
O:4
M:4
e:1
d:1
N:2
c:1
b:1
a:1
Post-order traversal:
a:1
b:1
c:1
N:2
d:1
e:1
M:4
O:4
f:1
R:1
In New Hampshire format:
(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;
```