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How to use E.T.E. a Python tree package within Sage?

asked 2013-01-19 03:04:51 -0500

Rolandb gravatar image

Hi, ETE is a Python based tree building package with nice graphical support. Can I use it within Sage? Thanks, Roland

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answered 2013-01-21 20:03:27 -0500

benjaminfjones gravatar image

updated 2013-01-21 20:04:19 -0500

I followed the instructions from the ETE webpage and it looks like you can install ETE inside the Sage shell environment (so that the python modules will be picked up by Sage), but it looks like there will be some optional dependencies missing:

> cd <TOP LEVEL SAGE DIRECTORY>
> ./sage -sh
> easy_install -U ete2

...

Installing ETE (A python Environment for Tree Exploration).

Checking dependencies...
MySQLdb cannot be found in your python installation.
MySQLdb is required for the PhylomeDB access API.
PyQt4 cannot be found in your python installation.
PyQt4 is required for tree visualization and image rendering.
lxml cannot be found in your python installation.
lxml is required from Nexml and Phyloxml support.

However, you can still install ETE without such functionality.
Do you want to continue with the installation anyway? [y,n]
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Asked: 2013-01-19 03:04:51 -0500

Seen: 452 times

Last updated: Jan 21 '13