Primer Design Tools     
AMOD a tool for designing antisense morpholino oligonucleotides
Array Designer can design hundreds of primer for DNA or oligonucleotide microarrays
ASePCR a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts
PCR Oligo Maker a tool for designing PCR probes based construction of long DNA molecules
autoprime amplifies  cDNA generated from mRNA but not genomic DNA
calculator Oligonucleotide Calculator
cDNA primers for creating primers around the Open Reading Frame of cDNAs
codehop primers designed from protein multiple sequence align
CODEHOP generates  Hybrid Oligonucleotide Primers; degenerate PCR primer design
DEQOR aids in the design and quality control of small interfering RNAs (siRNAs)
DINAMelt a tool for predicting hybridization and folding of DNA and RNA
DoPrimer web based primer design  
Electronic PCR Find STS map location in a DNA sequence of interest; useful for detecting mis-priming events
ELXR exon locator and extractor  
E-RNAi a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments
exon primer perl script design primers based on Perl script
ExonPrimer
helps to design intronic primers for the PCR amplification of exons 
FastPCR design of PCR primers for standard and long PCRs, inverse PCR
Gene2Oligo divides both strands of DNA sequence into a set of contiguous oligonucleotides
Genefisher nteractive primer design tool for standard or degenerate primers
GeneWalker allows you to work with two primer sequences simultaneously
genomic primer for creating primers around exons in genomic DNA
GenoPlante
For high-throughput design
MethPrimer Design Primers for Methylation PCRs
MuPlex a tool to assist in the design of multiplex PCR assays
Oligo Calculator oligo calculator
OligoArray2  computes gene specific oligonucleotides for genome-scale oligonucleotide microarray 
OligoChecker Verifies the Specificity of Batch Oligo Designs 
Oligodb generates oligos suitable for expression experiments
OligoPicker  picks specific oligos by skipping regions with contiguous bases common in other sequences. 
OligoWiz allows for the integration of sequence annotations
OligoWiz 2 Server intelligent design of oligonucleotides for DNA microarrays
PCR Guide guide
PCR now A Real-Time PCR Primer Design Tool
pcr suite collection of programs that interact with primer 3.0
PDA primer design
PerlPrimer open-source PCR primer design
Pride automatically designs primers
PriFi a tool for designing and evaluating primer pairs 
Primaclade accepts a multiple species nucleotide alignment file as input 
PRIMEGENS selecst gene-specific fragments and then design primer pairs using Primer3 for PCR amplifications
primer design list of primer software
Primer Generator an automated generator of primers for site-directed mutagenesis
primerbank a public resource for PCR primers
PrimerPremier design primer pairs for PCR and multiplex experiments
PrimerX Automated design of mutagenic primers for site-directed mutagenesis
primo from ChangBioscience
ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments
PROBEmer Primer Design for Target Families
ProbeWiz Server  predicts optimal PCR primer pairs for generation of  probes for cDNA arrays
ProMide  ProMide is a collection of command-line tools for Probe selection
PUNS assists in the specificity design of PCR primers
QPPD contains information about primer sets published for quantitative PCR
Sfold aiding the design of short interfering RNAs 
siDirect for computing siRNA sequences 
siRNA Selection Server design of short interfering RNAs (siRNAs) 
SNPbox does large-scale standardized primer design 
TGGE-star designs primers fulfilling the requirements for a sensitive mutation screening
TROD  for short interfering RNA (siRNA) synthesis with T7 RNA polymerase
Vector NTI PCR primer design
Visual OMP  multiplex primer and probe design optimized to reduce cross-hybridization. 
webprimer primer design