Table 1 Comparison of different primer design software programs

Multiplex PCR

Yes

Yes

Yes

No

No

No

Input

BED

FASTA

BED

FASTA

FASTA

FASTA

Web interface

Yes

No

No

Yes

Yes

No

Free for academics

Yes

No

Yes

Yes

Yes

No

Avoid SNPs in primers

Yes

Yes

Yes

–

No

No

Avoid primers in repeat areas

Yes

No

Yes

No

No

No

Single primer secondary structure check

Yes

Yes

No

Yes

Yes

Yes

Specificity checking alignment algorithm in the whole genome

Yes

No

No

No

Yes

No

Mutually compatible without secondary structure

Yes

Yes

No

–

–

–

Mutual specificity checking alignment algorithm in the whole genome

Yes

No

No

–

–

–

Self-defined species genome

Yes

No

No

–

Yes

–

Next-generation sequence addition

Yes

Yes

Yes

–

–

–

Graphic overview of primers found

Yes

–

No

No

Yes

Yes