Public Repository

Last pushed: 3 years ago
Short Description
Reproducible phylogenetisc python tools in IPython notebook
Full Description

ReproPhylo: Reproducible Phylogenetics

ReproPhylo is a reproducible phylogenetics pipeline written in python and making use of BioPython and other open tools. This is an implementation in IPython notebook

Galaxy version



ReproPhylo is in the public domain under a CC0 licence. This is a 'no copyright' licence and you are free to use, modify and repurpose any part of our work as you see fit. Some of the dependencies have more constricting licences. See the documentation for details.


Docs and guides are available in a public Google Doc, and you are encouraged to edit, extend and improve these docs if you wish.


We welcome your additions and improvements, just fork the repository on GitHub and then send a pull request.


For Windows and Mac go here
Install Docker


The shell script startRP can be downloaded from here and run as follows:


$ sh ./startRP /path/to/your/dir

It will start up the default web browser at the IPython notebook login page. The password is 'password'. More on this script in the manual.

Only files in the path you have specified will be accessible from within the container.

Cleaning up

The following script will stop the container and delete it. Files you have written in the session will remain in the path you have specified upon start-up.

$ sudo docker rm -f rpnotebook
Docker Pull Command