Tuesday, February 10, 2009

Large Scale Phylogenetic Rendering

The New York Times is running an article, "Crunching the Data for the Tree of Life":
For years now researchers have sequenced DNA from thousands of species from jungles, tundras and museum drawers. They have used supercomputers to crunch the genetic data and have gleaned clues to how today ’s diversity of species evolved over the past 450 million years. There’s just one problem. They have no way to visualize it...

The article mainly concerns itself with large scale phylogenetic analysis and rendering. The kind of rendering you would do with ATV or PAUP is for small sub branches of the total tree of life. This article analogizes the goals of these programs with Google Earth, programs that can quickly deal with large scale data sets.

One of the programs mentioned is Paloverde program from UC Davis(The site mentioned in the paper seemd to be down, but you can find a Arizona mirror to download the program).  They provide a compiled binary for Mac OSX.

Another program for this type of large scale rendering is Phlyo3D that works in conjunction with Walrus, a Java3D based graph rendering platform.

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