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/.