I will use PERL to create a set of command line programs for topological queries in BioSQL. The goal of this project is to create an interface that is suitable for high throughput creation and modification of SQL based phylogenies. I will use this interface to further my research on the classification of plant LTR retrotransposons.
This was a Google Summer of Code project in 2007, under the Phyloinformatics Summer of Code (NESCent) mentoring organization. The mentor was Hilmar Lapp. Full information and more documentation is available at the project homepage, which has been copied to the Github wiki for this project.