Comparison with other dyes
The Alexa series dyes are less pH-sensitive and more photostable than the original dyes (fluorescein, rhodamine, etc.) from which they were synthesized.
However, brightness comparisons are not presently available. Brightness is commonly measured as a product of extinction coefficient (absorption efficiency) and quantum yield (emission efficiency)  While extinction coefficients are known (see the table above), the quantum yields of the Alexas have not been published by Molecular Probes.
In one case, a third party has compared one Alexa with another commonly used dye. This was a comparison of Cy5 and its Alexa with similar wavelength, Alexa 647, with the dyes conjugated to DNA.  This study found that Cy5 is brighter, but less photostable than Alexa 647.
Therefore presently it is difficult to quantitatively choose the best dye for a particular application and in many cases empirical testing is in order.
The Alexa Fluor Dye Series. Molecular Probes, Inc. (2006-04-06). Retrieved on 2007-08-13.
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Berlier JE, Rothe A, Buller G, et al (2003). "Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates". J. Histochem. Cytochem. 51 (12): 1699-712. PMID 14623938.
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