BigPlant v2: Fully Automated Construction of a High Resolution Seed Plant Phylogeny

The BigPlant project (http://nypg.bio.nyu.edu/bp/) aims to construct a complete phylogenetic tree for all plant species with extensive sequence information. That first version of such a phylogenetic tree included over 100 taxa in which each was represented by at least 2000 genes. This version of the pipeline was semi-automated and required frequent user intervention. With the rapid increase availability of sequence information we envisioned the need to run the pipeline on a frequent basis and therefore aim to fully automate the process. The new improved pipeline now includes Data acquisition and formatting, Ortholog assignment, Construction of phlyogenetic matrix and Phylogenetic analysis in a single fully automated workflow. Further optimizations were made to accommodate larger data sets and decrease the computation load. In addition, post-phylogeny analysis stages are being integrated into the process. Finally, a brand new web-based and highly responsive, visualization tool was developed to allow biologists to explore the data in an interactive manner. This BigPlant TreeExplorer will allow users to mine the data rich phylogenetic matrix to derive and test hypotheses regarding the genetic mechanisms underlying observed traits. The TreeExplorer will be made available on the iPlant infrastructure to allow a large audience to reach it and integrate the visualization of phylogenetic context into their workflows.