bin/clone_filter bin/count_fixed_catalog_snps.py bin/cstacks bin/denovo_map.pl bin/gstacks bin/integrate_alignments.py bin/kmer_filter bin/phasedstacks bin/populations bin/process_radtags bin/process_shortreads bin/ref_map.pl bin/sstacks bin/stacks-dist-extract bin/stacks-gdb bin/stacks-integrate-alignments bin/tsv2bam bin/ustacks