Bioinformatic code for manuscript "Seasonal migration to the tropics promotes genetic diversity but not gene flow in boreal birds"

This dataset contains bioinformatic code used in the manuscript "Seasonal migration to the tropics promotes genetic diversity but not gene flow in boreal birds." This repository contains the bioinformatic pipeline steps we used to analyze raw sequence data, which are themselves hosted in the NCBI SRA. Steps are divided into different files and would be followed in the numbered order of their file names. The code in this repository is not designed to be ready-to-run, but rather to clearly indicate which steps were taken and which arguments were used with each command. Each file contains detailed notes about how each step was run (e.g., in SLURM array jobs etc), how files could be organized, and what a user would need to do to replicate these analyses. Some of the numbered scripts make use of additional un-numbered scripts which are included here. Un-numbered scripts are not run independently, but rather are run by commands within numbered scripts. This repository also contains the data underlying the figures in the associated manuscript, which are also in un-numbered .csv and .tre files.