Tuesday, 25th January, 2011, 12:00 pm

Analysis and manipulation of phylogenomic data using ETE

ETE is a python programming library that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It allows to read trees in Newick format and operate with them as very intuitive python objects, providing advanced methods to locate nodes, browse tree topology, annotate branches, or manipulate node connections. In addition, ETE provides a fully customizable system for tree visualization. Users can visualize trees interactively or write their own python functions to create tree images in PDF or SVG format.

Although ETE is mainly focused on phylogenetic analysis (i.e. connectors to the phylomeDB database, orthology and paralogy detection, tree reconciliation) it can be also used to deal with any type of data that can be represented as a hierarchical tree. For instance, microarray clustering results are phylogenetic profiles are well supported.

Starting from version 2.1, ETE will provide a new module to add interactive phylogenetic trees within web pages (see http://phylomedb.org/?q=search_tree&seqid=Phy00085K5_HUMAN for an example) and support for the PhyloXML and NeXML formats. Some ETE examples can be found at http://ete.cgenomics.org/examples

With this short tutorial I will introduce the most basic functionality and the potential use of the different ETE modules. A comprehensive practical course on ETE and related tools is scheduled by the beginning of March 2011.

Speaker: Jaime Huerta Cepas. Comparative Genomics Group. Bioinformatics & Genomics Programme. CRG

Room room 470 Sem 2