June 15th, 2015 - Bogota, Colombia The data included in this package was used for every analysis in the publication "A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing" by Simon Uribe-Convers, Matthew L. Settles, and David C. Tank, as part of Uribe-Convers' dissertation at the University of Idaho. The data is comprised of R scripts to mine and process RAW high-throughout sequencing (HTS) reads, molecular matrices of 48 chloroplast regions and 48 nuclear loci, and a combined chloroplast-nuclear dataset, an alignment of six complete chloroplast of six species of the plant genus Bartsia (Orobanchaceae), and alignments of three nuclear genes done with Sanger sequencing. The study includes the methodology to generate large quantities of HTS data using microfluidic amplification and Illumina sequencing, as well as traditional phylogenetic analyses performed with PartitionFinder, RAxML, GARLI, and MrBayes. It also contains a table with alleles occurrences in every locus for every sample. If you have any questions or comments, please do not hesitate to contact me at uribe.convers@gmail.com or at www.simonuribe.com. Best, Simon Uribe-Convers, Ph.D.