The primary repositories are ‘Exome Capture Probe Design‘ which is the pipeline I used to design capture probes from three transcripts of parachuting frogs (genus Rhacophorus).
Next I have ‘Probe Design Plethodon‘, which I used to design capture probes from a Plethodon cinereus transcript and the Ambystoma reference genome.
I have ‘Target Capture Analyses‘, which include scripts for trimming and preparing the target capture outputs from analysis pipelines.
Finally, I have ‘O’Connell et al. MPE Cyrts‘, which includes scripts for running the BioGeoBears analyses I used in the MPE paper here. I am going to start adding scripts and input files for each of my papers, so stay tuned for future repositories.