*NEW* Analysis and manipulation of phylogenomic data using ETE, Bioinformatics Training Course in Portugal


            Analysis and manipulation of phylogenomic data using ETE

       Deadline for applications: June 11th 2010
       Notification of acceptance dates:
            EARLY:June 2nd (on special request)
            NORMAL: June 12th 2010
       Course date: June 23rd – June 25th 2010

Course description:
Phylogentic analyses are gradually reaching genomic scales. Nowadays, many
resources and surveys encompass a large number of trees that, often, cannot be
manually analyzed. Bioinformatics toolkits are intended to provide a flexible
framework to deal with specific data in a programmatic way, thus facilitating
the analysis of large collections of data. The Environment for Tree
(ETE, http://ete.cgenomics.org) is a Python programming toolkit specially
focused on dealing with hierarchical trees. It allows, for instance,
to perform
a number of operations on phylogenetic trees, as well as designing automatic
pipelines. It also provides a highly customizable drawing engine, which can be
used to create complex annotated tree images in an automatic way or to
interactively explore single trees. Moreover, the ETE toolkit is not only
limited to large scale analyses, as it can be used to easily develop specific
tree analysis methods for single trees.
The purpose of this course is to provide an introduction to the analysis of
phylogenetic trees. It will cover a broad range of tasks that are usually
required in any phylogenomic analysis: tree rooting, prediction of orthology
and paralogy relationships, tree annotation, calculating distances among
sequences or species, tree pruning, trees comparison, and tree visualization.
The use of large scale phylogenomic resources, such as phylomeDB or Ensembl
Compara, will be also tackled through examples and exercises. This course will
be mostly practical and will be focused on solving real life examples.

Course Pre-requisites:
Course attendees are expected to have basic programming skills (not
in Python, although it is recommended*). All exercises will consist on
developing Python scripts to perform different analysis on phylogenetic trees
using the ETE toolkit on a GNU/Linux environment.

*Important Note: NO introduction to Python programming is scheduled in the
course. However, Python is a very intuitive language that can be learned
quickly when you have programmed in other languages. As a reference, Chapters
3-7 and 9 from this tutorial would be more than enough to follow the whole

Course fee: Eur 240.00 includes lunch, coffee-breaks, full documentation


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*NEW* RNA Bioinformatics, training course in Portugal

RNA researchers,
Do not miss the deadline if you are interested. This is a brand new course in RNA Bioinformatics, to be held in sunny Portugal in a really cost effective way!

Applications are open for the new GTPB Bioinformatics Training Course

RNA10                                                   Application Deadline
RNA Bioinformatics                                      Until June 22nd

Instructors: Paul Gardner, Anton Enright

Course dates: July 5th-9th 2010


This course will give an overview of RNA and aspects of the informatic
challenges associated with studying RNA. This course will be run as a mixture
of lectures and hands-on problem solving sessions.


The course is very practical in nature. After participating attendees will be
aware of the difficulties with dealing RNA. Current methods for addressing
these challenges and the limitations of each approach. In detail they should be
able to predict RNA secondary structures for given sequences, the should be able
to use state of the art RNA homology search tools, predict RNA:RNA interactions
and use comparative methods for studying RNA structure.

More information, as usual, at


Pedro Fernandes
GTPB Coordinator

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