[Biopython] ETE: a python Environment for Tree Exploration

[Jaime Huerta Cepas]

Hi all,

I have recently finished a software (ETE) that might be of your interest.

ETE (Environment for tree Exploration) is a python toolkit to analyze,
manipulate and visualize hierarchical trees. It allows to deal with any kind
of tree, but it includes specific data types for loading phylogenetic and
clustering trees. Besides many tree handling options it provides some
analytic methods such as orthology/paralogy prediction or cluster
validation. The toolkit is GPL and aims to be very flexible and
configurable, so it can be used together with other toolkits such as
BioPython.

The development of this software responses to the needs of our own group
during the last years, and I hope it can be now useful for the
bioinformatics community.
Bugs and comments are very welcome, as well as any idea for a better
integration with Biopython :)

program, documentation and examples can be found at http://ete.cgenomics.org

hope it's useful for you!

cheers,
Jaime

** Summary of main ETE's features: **

General trees
==========
Advanced node annotation, tree topology manipulation, automatic tree
prunning, cut \& paste partitions, trees concatenation, random trees
generation, iterate over leaves and descendants, pre and pos-order tree
traversion, root and unroot options, advanced nodes search,  get distances
among nodes, detect midpoint outgroup, find farthest descendant node, find
farthest node in the whole tree, detect first common ancestor among nodes,
text mode visualization, newick rendering (several formats), extended newick
format integration, support for built-in python operations: print,  len,
iter, in.

Phylogenetic trees
================
Link to multiple sequence alignments, automatic species name detection,
check node monophily, evolutionary events dating, detect orthology and
paralogy relationships: species overlap and tree reconciliation methods,
complete access API to the phylomeDB database, integrated visualization
(show molecular sequences and evolutionary events).

 Clustering trees
==============
link to numerical matrices, calculate inter and intra-cluster distances
among clusters, calculate Silhouette and Dunn Indexes, integrated
visualization (display numerical profiles in several formats).

Treeview extension
===============
Interactive Graphical User Interface (GUI), programmable drawing engine,
independent node aspect editing, support drawing node extra features (text
or external images),  vector graphics rendering using PDF format.


-- 
=========================
Jaime Huerta-Cepas, Ph.D.
CRG-Centre for Genomic Regulation
Doctor Aiguader, 88
PRBB Building
08003 Barcelona, Spain
http://www.crg.es/comparative_genomics
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