[Biopython] ETE: a python Environment for Tree Exploration

[Frederico Arnoldi]

Jaime,
Thanks for sharing. Very useful!
Frederico Arnoldi

> From: biopython-request at lists.open-bio.org
> Subject: Biopython Digest, Vol 81, Issue 21
> To: biopython at lists.open-bio.org
> Date: Fri, 18 Sep 2009 12:00:02 -0400
  
> Date: Thu, 17 Sep 2009 19:58:38 +0200
> From: Jaime Huerta Cepas <jhcepas at gmail.com>
> Subject: [Biopython] ETE: a python Environment for Tree Exploration
> To: biopython at lists.open-bio.org
> Message-ID:
> 	<c5882df30909171058t7fbd441aqb9ce64af82bc24e7 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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
> =========================
>

_________________________________________________________________
Você sabia que o Hotmail mudou? Clique e descubra as novidades.
http://www.microsoft.com/brasil/windows/windowslive/products/hotmail.aspx