| process_radtags.pl | Cleans raw Illumina reads, outputs FASTA/FASTQ files. | Raw Illumina reads | No |
| ustacks (unique stacks) | Builds loci de novo and detects haplotypes in one individual. | Cleaned FASTA/FASTQ files | No |
| cstacks (catalog stacks) | Merges loci from multiple individuals to form a catalog. | ustacks, tab-separated files | No |
| sstacks (search stacks) | Matches loci from an individual against a catalog. | ustacks and cstacks, tab-separated files | No |
| markers.pl | Calls mappable markers from parental loci. | None | Yes |
| index_radtags.pl | Indexes the database for use by the web interface. | None | Yes |
| denovo_map.pl | Executes ustacks on each individual, builds a catalog with cstacks, and matches individuals against the catalog with sstacks. Calls markers with markers.pl and indexes the database with index_radtags.pl. | Cleaned FASTA/FASTQ files | Yes |
| genotypes.pl | Calls genotypes in a map cross population and outputs markers for use by JoinMap or r/QTL. | None | Yes |
| pstacks (population stacks) | Takes cleaned reads aligned to a reference genome, builds stacks based on the genomic locations of the reads, and detects haplotypes in one individual. | Bowtie or SAM sequence alignments | No |
| ref_map.pl | Executes pstacks on each individual, builds a catalog with cstacks, and matches individuals against the catalog with sstacks. Calls markers with markers.pl and indexes the database with index_radtags.pl. | Cleaned FASTA/FASTQ files | Yes |
| sort_read_pairs.pl | Given a set of Stacks data and a set of cleaned, paired-end Illumina reads, outputs one FASTA file for each stack consisting of the paired-end reads associated with reads in that stack. | ustacks output files, cleaned FASTA/FASTQ files | No |
| load_sequences.pl | Loads a set of loci-associated sequences (e.g., RNA-seq ESTs) into the database. | FASTA file containing sequences | Yes |
| export_catalog.pl | Exports sequences from the database, including loci and loci-related sequences. | None | Yes |