STACKS output from the correction module (rx_stacks) of ref_map (two PRG: PRG_AmericanCrow and PRG_ZebraFinch) and de_novo (run 1 and run 2 separate: Denovo_R1 and Denovo_R2) pipelines and populations maps used (Cy_2POP.txt and Cy_3POP.txt). Included are the catalog.tags, de-novo assemblies and output of the populations module. Each directory includes summary statistics per locus and overall, and all SNP data in STRUCTURE, FASTA, Genpop, PLINK and VCF format.