Another major focus of our research is the development of software tools to facilitate and enhance our understanding of the underlying evolutionary processes shaping diversity in pathogen populations. The evolutionary toolkit developed in our laboratory (SNAP Workbench) makes population genetic analyses tractable and accessible to the biologist. A key aspect to managing and integrating DNA sequence-based variation with phenotypic data is to recognize the hierarchical nature of DNA sequence variation. This hierarchical organization implies a process driven system that is most accurately captured using evolutionary approaches.
We have been implementing new and existing methodologies and tools to examine the influence of mutation, recombination, gene flow, selection and demography on the evolution of fungal genomes, populations and species. Our workbench effectively manages and integrates a plethora of new approaches for making inferences on population processes from DNA sequence variation, bringing together simple summary-statistics, nonparametric methods and complex parameter-rich models. A long-term goal is integrating user-interactive tutorials in our workbench for teaching and training on these methods.
Recently we have been migrating our stand-alone SNAP tools to a web portal to allow computationally intensive programs to execute on multiple compute nodes. The portal is housed on NCSU's High Performance Computing (HPC) cluster and will be accessible to NCSU faculty and students with unity access. The portal manages high throughput data and analyses via pipelines to facilitate public use and downstream analyses. Previously this was not possible using the stand-alone version. The portal also eliminates cross platform incompatibilities and promotes campus-wide sharing of HPC resources.