This script extract sequence haplotypes from the “alleles.tsv” files generated by STACKS and does some light filtering (you may want to add more). It’s very similar to the one I used for our 2013 Molecular Ecology paper, and still has some Great Sand Dunes-specific parameter names, but should work ok for other data sets. Oh, and I was using the “pstacks” reference-guided workflow in a slightly older version STACKS, in case that matters.

extract_haplotype_sequences_v4_annotated.r

example_alleles.tsv

Please let me know if you use this script and whether it needs tweaking.