Trait Evolution Progress Report
Trait Evolution Progress Report
Summary
Status
(see also iPToL Progress Report)
The group decided to use the implementation of Phylogenetically Independent Contrasts from Joe Felsenstein's software package PHYLIP. This first tool was included in the 2.0 release of the Discovery Environment in April 2010. After a hiatus of approximately 9 months, the working group resumed its activities. The group opted for the integration of functions from the R packages ape and geiger that implement the methods identified as a priority by the working group. The execution framework to support R scripts has been developed and discrete and continuous ancestral character reconstruction methods have been integrated into the Discovery Environment through the ape function ace and as part of the 3rd release of the DE (March 2011). The model fitting functions of the package geiger are currently being integrated. More tools have been identified and integrated, and will be part of the 0.4 release (OUCH, PICANTE, Disparity through time, Dating with penalized likelihood, lopper). Additionally, members of the group have integrated tools to retrieve and align sequences (GetSeq, Muscle) build (PROTPARS, DNAPARS, DNAML, PROML , PROTNJ , DNANJ, RAxML - DNA, RAxML -Protein, Ninja, Phyml, FastTree) and visualize phylogenetic trees (iPlant's tree viewer). Together with the analysis tools, this formed a proof-of-concept complete phylogenetic workflow that could be presented at the BSA and ASPB conferences.
The group decided to tackle the problem of numerical optimization in R which affect virtually all the R-based tools integrated so far. Simply stated, the group noticed that under certain conditions, many optimization algorithms returned invalid results. A statistics student has been hired to work on the problem. The Working Group has also started an EOT effort in collaboration of the Dolan DNA Learning Center and has started collecting example data sets to be used to teach evolution in different contexts (e.g. ecology, plant physiology).