Justin C. Bagley, September 11, 2017, Richmond, VA, USA
This markdown note describes how I used several software programs to process and eventually analyze SNPs from ddRAD tag loci (contigs) in SNAPP (Bryant et al. 2012), which is implemented in BEAST (Drummond et al. 2012; Bouckaert et al. 2014) and is of broad interest in evolutionary biology for inferring species trees (e.g. Demos et al. 2015; Stange et al. 2017). I provide a perspective based on my experiences analyzing data generated using Next-Generation Sequencing on ddRADseq genomic libraries prepped for several species/lineages of Neotropical freshwater fishes from the Brazilian Cerrado (Central Brazil).
My account is given in first person and represents merely one way to analyze data in SNAPP; there are other approaches, and other documents (e.g. this BFD* tutorial; L
