ProbeDealer is a convenient tool for designing probes for highly multiplexed DNA/RNA fluorescence in situ hybridization (FISH) and conventional single-molecule RNA FISH. For the latter, please refer to a special instruction here.
Reference: Mengwei Hu*, Bing Yang*, Yubao Cheng, Jonathan S.D. Radda, Yanbo Chen, Miao Liu & Siyuan Wang, Scientific Reports, Volume 10, Number 22031, (2020). *Co-first authors. (Link to paper).