University of Glasgow

Roderic Page

Following on from the [SVG
experiments](http://iphylo.blogspot.com/2012/12/svg-experiment.html)
I\'ve started to put some of the Javascript code for displaying
phylogenies on Github. Not a repository yet, but as
[gists](https://gist.github.com/), little snippets of code. Mike Bostock
has created <http://bl.ocks.org/> which makes it possible to host gists
as working examples, so you can play with the code \"live\".  
  
The [first gist](https://gist.github.com/4224658) takes a Newick tree,
parses it and displays a tree. You can try it at
<https://bl.ocks.org/d/4224658/>.  
  
The [second gist](https://gist.github.com/4229068) takes a basic NEXUS
file containing a TREES block and displays a tree (try it at
<http://bl.ocks.org/d/4229068/> ). You can grab examples NEXUS tree
files from [TreeBASE](http://www.treebase.org) such as [tree
Tr57874](http://purl.org/phylo/treebase/phylows/tree/TB2:Tr57874?format=nexus).  
  
![Nexus](http://lh4.ggpht.com/-B_JL6Qw3HJ8/UMEjcu3ISvI/AAAAAAAACT4/h-m2j_wrNU8/nexus.png?imgmax=800 "nexus.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550" height="441"}**Why am I doing this?**  
Apart from \"because it\'s fun\" there are two reasons. The first is
that I want a simple way to display phylogenetic trees in web pages, and
doing this entirely in the web browser (Javascript parses the tree and
renders it in SVG) saves me having to code this on my server. Being able
to do this in the browser opens up the opportunity to embed tree
descriptions in HTML, for example, and have the browser render the tree.
This means the same web page can have machine-readable data (the tree
description) but also generate a nice tree for the reader. As an aside,
it also shows that TreeBASE could display perfectly good, interactive
trees without resorting to a Java appelet.  
  
The other reason is that the web seems to be moving to Javascript as the
default language, and JSON as the standard data format. Instead of large
chunks of \"middleware\" (written in a scripting language such as Perl,
PHP, or, gack, Java) which is responsible for talking to databases on
the server and sending static HTML to the web browser, we now have
browsers that can support sophisticated, interactive interfaces built
using HTML and Javascript. On the server side we have databases that
speak HTTP (essentially removing the need for middleware), store JSON,
and use Javascript as their programming language (e.g., CouchDB). In
short, it\'s [Javascript, Javascript,
everywhere](http://architects.dzone.com/articles/javascript-javascript).  


Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repository yet, but as gists, little snippets of code. Mike Bostock has created http://bl.ocks.org/ which makes it possible to host gists as working examples, so you can play with the code "live".  The first gist takes a Newick tree, parses it and displays a tree.

Messaggi di Rogue Scholar

NEXUS parser and tree viewer in Javascript