README.md

fly population genomics scripts

Data available from NCBI SRA BioProject: PRJNA285429

Associated publication: Graves Jr, J.L., Hertweck, K.L., Phillips, M.A., Han, M.V., Cabral, L.G., Barter, T.T., Greer, L.F., Burke, M.K., Mueller, L.D. and Rose, M.R., 2017. Genomics of Parallel Experimental Evolution in Drosophila. Molecular biology and evolution, 34(4), pp.831-842.

Linkage disequilibrium (LD) using LDx

• implements scripts to run LDx using slurm

Transposable elements using popoolationTE

• creates necessary files and runs popoolationTE to identify de novo TE insertions from pooled population sequencing