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README.md

ivy: interactive visual phylogenetics

ivy is a lightweight library and an interactive visual programming environment for phylogenetics. It is built on a powerful foundation of open-source software components, including numpy, scipy, matplotlib, and IPython.

ivy emphasizes interactive, exploratory visualization of phylogenetic trees. For example, in IPython:

from ivy.interactive import *

root = readtree("primates.newick")
fig = treefig(root)

This will open an interactive tree window that allows panning, zooming, and node selection with the mouse. Additionally, you can manipulate the figure from the console, e.g.:

fig.ladderize()
fig.toggle_leaflabels()

Documentation and other resources

(Out of date and incomplete)

http://www.reelab.net/ivy

Installation

Recommended for non-developers: use conda for Python 3.

  1. Download and install Miniconda for Python 3

    https://conda.io/miniconda.html

    The following assumes conda is now in your $PATH.

  2. Create an environment for ivy:

    conda create -n ivy ipython jupyter numpy scipy matplotlib biopython pillow pyparsing pytz pandas lxml
  3. Activate the environment:

    source activate ivy
  4. Install ivy:

    pip install https://github.com/rhr/ivy/zipball/master
  5. To update, uninstall it first:

    pip uninstall ivy-phylo

    then re-run pip as above.

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Interactive Python shell for visual phylogenetics

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