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User’s Guide

ivy is designed to be used both as a library and interactively, in the IPython shell. IPython is an enhanced Python interpreter designed for interactive and exploratory scientific computing.

This screencast demonstrates some basic concepts:

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Starting the shell

The -pylab option starts IPython in a mode that imports a number of functions from matplotlib and numpy, and allows interactive plotting.

$ ipython -pylab

In interactive mode, ivy provides some useful shortcut functions (e.g., readtree, readaln, treefig, alnfig) that you will typically want to import as follows.

In [1]: from ivy.interactive import *

Viewing a tree

Assuming you have started the shell,

In [2]: s = "examples/primates.newick"
In [3]: fig = treefig(s)

Here, the variable s can be a newick string, the name (path) of a file containing a newick tree, or an open file containing a newick string. Note that file paths are completed dynamically in ipython by hitting the <TAB> key, making it easy to find files with little typing.

A new window should appear, controlled by the variable fig. View the help for fig:

fig?