A method of identifying a nucleotide in a nucleic acid sequence, comprising: receiving, at a computer system, a first optical signal from a reaction that produces optical signals in response to incorporation of a nucleotide analog in a template dependent primer extension reaction, wherein the first optical signal is emitted from a fluorescent label on a polyphosphate chain of a nucleotide analog, and the fluorescent label is liberated from the nucleotide analog during an incorporation of the nucleotide analog in the template dependent primer extension reaction; classifying, using the computer system, the first optical signal as a significant pulse based on an optical pulse width of the first optical signal and an intensity of the first optical signal; associating, using the computer system, the first optical signal with a spectrally distinguishable signal profile that correlates to a particular dye spectrum; when the first optical signal is (i) deemed a significant pulse by the classifying and (ii) is associated with a spectrally distinguishable signal profile by the associating, determining whether the first optical signal is an incorporation event based upon a signal environment around the first optical signal, wherein the signal environment includes a characterization of an optical signal preceding the first optical signal or a characterization of an optical signal that comes after the first optical signal; and identifying, using the computer system, the nucleotide in the nucleic acid sequence when the optical signal is determined to be an incorporation event. receiving, at a computer system, a first optical signal from a reaction that produces optical signals in response to incorporation of a nucleotide analog in a template dependent primer extension reaction, wherein the first optical signal is emitted from a fluorescent label on a polyphosphate chain of a nucleotide analog, and the fluorescent label is liberated from the nucleotide analog during an incorporation of the nucleotide analog in the template dependent primer extension reaction; the first optical signal is emitted from a fluorescent label on a polyphosphate chain of a nucleotide analog, and the fluorescent label is liberated from the nucleotide analog during an incorporation of the nucleotide analog in the template dependent primer extension reaction; classifying, using the computer system, the first optical signal as a significant pulse based on an optical pulse width of the first optical signal and an intensity of the first optical signal; associating, using the computer system, the first optical signal with a spectrally distinguishable signal profile that correlates to a particular dye spectrum; when the first optical signal is (i) deemed a significant pulse by the classifying and (ii) is associated with a spectrally distinguishable signal profile by the associating, determining whether the first optical signal is an incorporation event based upon a signal environment around the first optical signal, wherein the signal environment includes a characterization of an optical signal preceding the first optical signal or a characterization of an optical signal that comes after the first optical signal; and when the first optical signal is (i) deemed a significant pulse by the classifying and (ii) is associated with a spectrally distinguishable signal profile by the associating, determining whether the first optical signal is an incorporation event based upon a signal environment around the first optical signal, wherein the signal environment includes a characterization of an optical signal preceding the first optical signal or a characterization of an optical signal that comes after the first optical signal; and identifying, using the computer system, the nucleotide in the nucleic acid sequence when the optical signal is determined to be an incorporation event.