Are there any alternatives to Cy5?

Yes, there are a couple of alternatives to Cy5. Cy5 is one of the most widely used cyanine dye for labeling DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH).

DY647, a dye by DyLight™ is one alternative to Cy5. The performance, and absorption and emission spectra are similar to that of Cy5.

Allophycocyanin (APC) is another alternative to Cy5 but it is used almost exclusively in flow cytometry.

iFluor® 647 family has the spectral properties essentially identical to those of Cy5® (Cy5® is the trademark of GE Healthcare). Compared to Cy5 probes iFluor® 647 family has much stronger fluorescence and higher photostability. Their fluorescence is pH-independent from pH 3 to 11. These spectral characteristics make this new dye family an excellent alternative to Cy5® and Alexa Fluor® 647 (Cy5® and Alexa Fluor® are the trademark of Invitrogen and GE Health Care).