Update1 – 12/19 – Data for this paper seems to be unavailable – not sure why – but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there. Note – this is one reason that all data sets should be made available at the journal or third party sites.
OK never mind that the terminology of “functional phylogenomics” is a tiny bit vexing to me (long story – some other time perhaps). The paper behind it – PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.
1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)
2. Constructed a “total evidence” phylogeny for these taxa (using a few approaches)