Analysis code used for the following studies:
Baca, S.M., Alexander, A., Gustafson, G.T. and Short, A.E., 2017. Ultraconserved elements show utility in phylogenetic inference of A dephaga (C oleoptera) and suggest paraphyly of ‘Hydradephaga’. Systematic Entomology, 42(4), pp.786-795.
Gustafson, G.T., Alexander, A., Sproul, J.S., Pflug, J.M., Maddison, D.R. and Short, A.E., 2019. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecology and Evolution.
Gustafson, G.T., Baca, S.M., Alexander, A.M. and Short, A.E., 2020. Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance. Systematic Entomology, 45(3): 552-570.