ETE: a Python Environment for phylogenetic Tree Exploration

ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.

IPython Notebook integration

ETE has now support for inline image visualization when using the Ipython Notebook! To use it, just call the ETE tree render function using the keywork %%inline as a file name:

tree.render("%%inline", ... )

 

(requires ete2.2rev1026 or higher)

ETE 2.2 released

A new ETE version (2.2) is now available. It includes several new features and bug fixes. Most notably,

- A new EvolTree class type, developed by Francois Serra (at CNAG), which can be used to run adaptation tests and visualize results directly on tree branches and alignments.

- Several new face types are available to plot sequence domains, PieCharts and Barplots (see extended changelog for some examples)

- The TreeKO method (Marcet-Houben and Gabaldón, 2011), used to render all species trees derived from a duplicated gene family tree, has been ported and optimized as a built-in function of the PhyloTree class.

- The core Tree object includes some new features, such as a robinson-foulds metric function, new traversing methods including the iteration of node ancestors, custom collapsing options, an improved tree pruning method, and several function to resolve polytomies and check the monophyly of custom attributes within a given node.

 

 

New version: ETE 2.1

ETE 2.1 is available to download

COURSE: Analysis and manipulation of phylogenomic data using the ETE python toolkit and TreeKo


Organized by the Bioinformatics Core Facility at CRG and Toni Gabaldon's lab. Location: Centre for Genomic Regulation,  Barcelona (Spain).   Duration: 3 days  Dates:  April 6th- 8th (2011

free registration (limited places) deadline: (CLOSED)

(Added some location and accomodation info)

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