This repository contains instructions on handling target-enrichment (bait-capture) data using HybPiper and performing subsequent phylogenetic analyses on the Smithsonian Institution HPC (Hydra cluster). If you don't have your own dataset, you can use tutorial data from here. If you don't have access to the cluster, install all dependencies and programs used here such as MAFFT, TrimAl, RAxML on your system and run the main commands from the job files. Follow steps in the Data_processing.md.
Paper:
Vatanparast, M., A. Powell, J. J. Doyle, and A. N. Egan. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. Applications in Plant Sciences 6(3): e01036
Datasets are available from Figshare: https://doi.org/10.6084/m9.figshare.c.4040372.v4
Example phylogenetic trees using different species tree reconstruction methods.
