Uncompromisingly Flexible Phylogenetic Trees in Javascript, powered by d3
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TidyTree is both a full-featured web application for users, along with the underlying library for developers.
It's designed to replicate much of the functionality of FigTree, though it's by no means a perfect replacement. It does, however, run entirely in-browser.
First import the library:
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://unpkg.com/[email protected]/dist/tidytree.min.js"></script>(It requires d3!)
Then stick this in an HTML script tag:
let newick = "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);";
let tree = new TidyTree(newick, { parent: "body" });And Voila! Your body will be populated by a phylogenetic tree.
tidytree is based on this gist (See in action), which "mostly just duplicates the cannonical[sic] d3.tree and d3.cluster bl.ocks by Mike Bostock."
MicrobeTrace needed a Phylogenetic Tree renderer that enabled rerooting and distance scaling. Additionally, there were a bunch of nice-to-haves, like Unrooted and Circular views, Zooming, Colorable and Selectable nodes... You get the idea.
As for the viewer, well, we needed a platform to rapidly prototype features for the library. The product of that is a single-page web application that leverages literally all of the features of the library. If you're a dork like me, you can see this in the coding of the index.html file. Notice how all of the select widgets are programmatically populated--that's so we could implement new features (e.g. layouts) without having to update the Demo HTML. After that, all we had to do was keep the UI clean.
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