[PaperReview] An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies

One thing I didn’t do last year on this blog is reviewing papers. The reason is not just that I was lazy, but probably I put too much effort into one review post. That makes the post become a burden, and frequency of writing reviews reduced. So, keeping review articles simple enough looks important. The purpose of review posts on this blog is archiving what I think interesting and worth sharing with others. Over-emphasis of details is not necessary for this purpose.

I will re-start writing reviews of bioinformatic papers keeping this in mind.

Iwasaki, W., Takagi, T. (2010) An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies. Syst. Biol. 59(5): 584-593. doi: 10.1093/sysbio/syq044

Visualizing the information of multiple conflicting phylogenetic trees is a difficult task. The phylogenetic network is maybe the most frequently used, but its visual interpretation is not always straightforward. The Iwasaki&Takagi (2010) paper proposed an alternative method, called “centroid wheel tree”, to do this task.

The centroid wheel tree (CWT) is based on a consensus tree of multiple trees. One difference from the ordinal consensus is orders of branches. Instead of placing them randomly, branches descending from an unresolved node are placed in a order where more often grouped branches are placed closer. This circular ordering on a node and numbers between branches present the information of frequency of occurrence of clades. Once you get used to how to read a CWT, you find it contains most information you need to interpret results of phylogenetic analyses.

I&T2010.F3.large

Interpretations of notations on a centroid wheel tree. From Iwasaki & Takagi (2010). See http://sysbio.oxfordjournals.org/content/59/5/584/F3.expansion.html for details.

I think CWT is one of the best phylogenetic methods I have seen. It visualizes complicated information in a simple, but informative way. However, it is not very widely used, unfortunately. (At least, I haven’t seen CWTs in any phylogenetic litereture.) A possible reason is that it is not implemented in major phylogenetic analysis packages or simply it is not known by biologist community.

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