# TSRevolution
scripts for examining the evolution of target-site resistance, including:

running [argweaver](https://github.com/jkreinz/TSRevolution/blob/main/argweaver.sh), [relate & clues](https://github.com/jkreinz/TSRevolution/blob/main/relate_n_clues.sh) (and upstream [phasing](https://github.com/jkreinz/TSRevolution/blob/main/readback_popphasing.sh), [ancestral allele calling](https://github.com/jkreinz/TSRevolution/blob/main/multiple_alignment_ancestralstates.sh)), performing [tree-based tests for selection](https://github.com/jkreinz/TSRevolution/blob/main/selectiontests_overtwotimescales.R), [sweep scans](https://github.com/jkreinz/TSRevolution/blob/main/get_sweepscans.sh), and [LD analyses](https://github.com/jkreinz/TSRevolution/tree/main/LD_analyses).