| alphcont | DNA alphabet content reporting. | Getting base composition values (e.g. %GC, runs of bases). Numbers can be used for filtering or as features for sequence analysis. |
| blastout | BLAST output parser | Extracting seqs, coords, scores. Compiling alignments into metrics (e.g. specificity screens) |
| comp_seq | Comparing sequences using simple alignments. | Evaluating various similarity, complementarity metrics between primers, probes, etc. Used for oligo design and QC. |
| dna_util | Sequence slicing and dicing. Includes complexity metrics. | Sequence manipulations (e.g. rev comp, reformatting, masking, probe tiling, etc). Complexity metrics useful for filtering and sequence analysis. |
| filter | Simple line-based numerical filter. | Extracting subsets of sequence or data files with specific values. |
| gen_seq | Generate sequences. | Constructing enumerated or random sequence sets, with optional composition constraints. Sequences can serve as starting points for probe or index designs. |
| numstat | Simple line-based numerical stats tool. | Quick evaluation of numbers (e.g. mean, sd, percentiles, etc). Includes text-based histogram plotting. |
| pick_seq | Select sequence subsets, minimizing pairwise metrics. | Selecting orthogonal sequence sets, for example indexes or hybridization probes. Can separately weight similarity, complementarity metrics. Simple or Hamming alignments. |
| scoretab | Data table and number manipulations. | Manipulating data tables (e.g. bounding, scaling, subset extraction, etc.). Generating scores from values (e.g. map oligo Tm to range 0-1 via transfer function). Includes genetic algorithm operators. |
| seqtweak | Modify input sequences. | Introducing "mutations" into supplied sequences. Can randomly or systematically introduce SNVs and/or InDels. This is useful for simulations and some design tasks. |
| tm_util | Thermodynamic calculator, including extraction of sub-seqs. | Calculates Tm, dG, fraction hybridized using various nearest neighbor models. Useful for extracting candidate oligos with specific thermodynamic properties (e.g. lengh 15-25 and Tm 60-62). |
| venpipe | Wrapper for secondary structure and energy calculations. | Wraps Vienna package folding code, reporting oligo structure(s) and energy(s). Used for oligo design and QC. |
| wordfreq | Tallies DNA words (n-mers). Includes word-based scoring. | Tallying n-mers. Frequency tables derived from genomes, sequence libraries, etc. are useful to investigate uniformity or biases, and may be used to score novel sequences. |