This is a workflow that allows easily using a number of population structure analysis tools, with the goal to streamline workflows that allow easy comparison between methods and approaches. The original reason was to compare EEMS with other methods.

• EEMS
• flashpca
• admixture
• pong visualization of admixture
• TESS3
• treemix
• Spacemix
• conStruct
• FST (using plink)

Genotypic data is stored in plink format. Metadata/location data is stored using John Novembre's PopGenStructures data format, with some minor (recommended) changes. The pipeline is implemented using Snakemake, using python for most data wrangling and R for most plotting

As some of the data used requires permission, we are not free to redistribute it. To re-generate all figures from the paper, it will be necessary to

1. acquire access to all data and create master data set as described in the merge-pipeline
2. change paths in config/config.json to reflect your working environment
3. run snakemake all