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:
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 : from ivy.interactive import *
Assuming you have started the shell,
In : s = "examples/primates.newick" In : 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: