Compiling RAxML to Javascript using emscripten

[Terry Jones]

Has anyone else thought about compiling RAxML to Javascript using emscripten (http://kripken.github.io/emscripten-site/)?  I managed to do it today (on Mac OS X 10.13.4) and only needed to comment out one line of code to make it build cleanly. I'm not sure how to use it yet, though. I'm hoping there's a function I could pass an alignment (already in memory) to, rather than have it try to read from the filesystem. emscripten can simulate a filesystem, but you need to have the file data in advance to build into the fake filesystem. It would be nice to build something where a user could either upload a file or drag one onto a web page, this would then be read & a suitable data structure made to pass to the RAxML javascript.  I.e., avoid the main() function and the filesystem.

I thought I'd ask if anyone else has done something like this. It may seem like an odd to want to do, but I'd like to build an interactive exploration of some phylogenetics work and to do it in the browser using something like Observable (https://beta.observablehq.com/) and a JS library that can display trees given in Newick. So the idea isn't to build trees from large alignments as fast as possible, but rather to interactively show people how adding more sequences (or whatever) changes that tree that is built.

Regards,

Terry Jones

[Alexandros Stamatakis]

This sounds interesting, I am not aware of anybody else having done that
before. You may want to consider using RAxML-NG for this though.

Alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org