Materials from various workshops I have organized and contributed to. Workshop materials are normally sufficiently detailed to serve as stand-alone tutorials. In general the most recent workshop will have the most up-to-date information, but each workshop is slightly different, and the older materials should still contain some useful information.

RADSeq Assembly and Analysis

RADCamp workshops are designed to introduce ipyrad, a unified and self-contained RADSeq assembly and analysis framework, which emphasizes simplicity, performance, and reproducibility. In these workshops we proceed through all the steps necessary to assemble a typical RADSeq dataset. Additionally, we introduce the ipyrad ‘analysis’ API which provides a powerful, simple, and reproducible interface to several widely used methods for inferring phylogenetic relationships, population structure, and admixture.

Model-based inference in Phylogeography from single species to communities

CompPhylo workshops are designed to introduce a myriad of tools for making statistical inference about historical processes using genetic/genomic data. After introducing statistical approaches in model-based inferences, participants are be introduced to inference frameworks that span taxonomic scales from single-species demographic inference, to multi-species comparative analysis, to inference at the scale of the whole community. Participants also get hands on experience using approximate Bayesian computation, supervised machine learning and composite likelihood methods for model comparison.