Revision as of 04:50, 20 May 2009
BioGeography is a module under development by Nick Matzke for a Google Summer of Code 2009 project. It is run through NESCENT's Phyloinformatics Summer of Code 2009. See the project proposal at: Biogeographical Phylogenetics for BioPython. The mentors are Stephen Smith (primary), Brad Chapman, and David Kidd. The code currently lives at the nmatzke branch on GitHub, and you can see a timeline and other info about ongoing development here.
Abstract: Create a BioPython module that will enable users to automatically access and parse species locality records from online biodiversity databases; link these to user-specified phylogenies; calculate basic alpha- and beta-phylodiversity summary statistics, produce input files for input into the various inference algorithms available for inferring historical biogeography; convert output from these programs into files suitable for mapping, e.g. in Google Earth (KML files).