Sunday, January 29, 2012

One old, one new - a few phylogeny papers worth checking out

Just a quick one here. A few days ago in my lab we were discussing some challenges with doing phylogenetic diversity (PD) measurements in very very large phylogenetic trees. PD is a measure of total branch length in a phylogenetic tree for a group of taxa ... and we use it for many purposes.

For many of our applications we have been using an algorithm described by Mike Steele "Phylogenetic diversity and the Greedy Algorithm". But alas, is is not keeping up with the massive tree sets we are dealing with. Fortunately Aaron Darling in my lab found a alternative paper with a perfect sounding title for us: Phylogenetic Diversity within Seconds from Minh, Klaere, and von Haeseler. This seems like it will do the trick. I note - Kudos to Systematic Biology for making some older papers freely available. Not sure of their general policies on this but good to see.

Anyway - back to the grind ...

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