Challenges in phylogenetic tree visualization

I recently read an excellent review by Roderic Page, on the challenges in phylogenetic tree representation and visualization. It provides an overview  on existing software and tools (although he missed our ETE package, see image below for an example of ETE's visualization features). The number and diversity of existing tools is overwhelming, but probably matches the diversity of different interests and possible applications of phylogenetic trees. One may be interested in  overlaying sequence information (see below), while other would be interested in displaying information on the geographical distribution of the species. Some may need to represent uncertainty and overly different topologies, or networks to represent transfers of genetic material, the possibilities are unlimited.

 Most importantly he mentions some of the challenges of tree visualization software such as the ability to represent huge trees and to allow interactive behavior with the user. In our group we have encountered such needs and this is the reason behind implementing more visualization features in ETE. Fortunately new technologies are offering new opportunities as well, and I enjoyed imagining the possibilities that 3D visualization and touchscreen technologies will provide to researchers. Definitely is a field to follow.

 If you are interested in the topic. I recommend this video.

Educational video on the Tree of Life

In the blog of Jun-Hoe Lee, a former visiting student in my lab, I found this interesting video from Yale university on the Tree of Life and the efforts to reconstruct it.

  

I think it is a good piece for popular communication of science and conveys pretty reasonably well the problem. Of course, there are simplifications and some important aspects such as that of horizontal transfer of genes, symbioses, and their effects on the tree are not covered, but it provides an attractive and educational introduction to the problem of assembling the tree of life. 

Article collection on the Tree Of Life in Biology Direct

The journal Biology Direct has initiated an article collection entitled "Beyond the tree of Life". The main focus of this series seems to be the challenges posed by evolutionary mechanisms, such as Horizontal Gene Transfer, that may blur or completely destroy the classical view of a bifurcating tree of life representing the evolutionary relationships of organisms, specially prokaryotes.

 The issue is not new, but the current wealth of genomic data and the availability of new methodological approaches to measure and compare the evolutionary signals of thousands of protein families has prompted a revival of the debate on how strong are tree-like and network-like signals in the different domains of life.

The series started last June and is being updated regularly. There are already interesting articles from various authors including William Martin, Eric Bateste, and Eugene Koonin.

A nice add-on, which is one of the features I lke the most about Biology Direct, is that reviewer's reports can be read along with the paper, thus having a complementary view of the author's interpretation of the data.

Brief introductory article to phylogenomics

I would like to share a brief introductory article to Phylogenomics and Genome Evolution that I wrote by request from the Roche Institute portal. The idea was to provide an overview to the general audience of what is phylogenomics about and what are the main challenges ahead.

The article is also available in Spanish.

A PLoS currents for the Tree of Life

 I recently discovered that PLoS Currents has opened a new track for the Tree of Life: PLoS Currents: Tree Of Life.

 PLoS currents is yet another form of publishing scientific results. A small group of editors and reviewers reviews every paper to check that it is t is " a legitimate work of science and does not contain any obvious methodological, ethical or legal violations." If that's the case papers are published immediately (and indexed in Pubmed). Another novelty is that all the publication procedure is based on a web-based tool called google-knol.

 So far there are only 4 articles (or "knols"?) and they all seem pertinent to the topic, one of them was very useful to me, since it described a compilation of benchmark datasets for phylogeny. 

 It looks worth to keep an eye.