These are workflows and tutorials for the analysis of target capture sequence data to produce phylogenomic hypotheses.
It may be most useful to read the workflows in order, starting with 1 and finishing with 4.
Many of these workflows rely on the pipeline HybPiper (Johnson et al) so you are encouraged to first get familiar with the very good and detailed documentation produced by the authors of this pipeline. The main documentation can be found here: https://github.com/mossmatters/HybPiper and here: https://github.com/mossmatters/HybPiper/wiki/.
Although I write the workflows, many people have contributed over the years by suggesting or testing commands and giving me feedback, including Cassia Bitencout, J. Cid Vian, J. Kim, Ben Kuhnhäuser, Paola de Lima Ferreira, Grace Flanagan, O. Maurin, Bruce Murphy, V. Pérez Calle, O. Pérez Escobar, L. Pokorny, Zhi Qiang Shee, A. Zuntini.