This invention relates to a device for the determination of the sequence of nucleic acids and other polymeric or chain type molecules. Specifically, the device analyzes a sample prepared by incorporating fluorescent dyes at the end of copies of varying lengths of the sample to be sequenced. The sample is then vaporized, charged and accelerated down an evacuated chamber. The individual molecules of the sample are accelerated to different velocities because of their different masses, which cause the molecules to be sorted by length as they travel down the evacuated chamber. Once sorted, the stream of molecules is illuminated causing the fluorescent dyes to emit light that is picked up by a detector. The output of the detector is then processed by a computer to yield of the sequence of the sample under analysis. The present invention improves over the prior art by using photo-detection of the individual molecules instead of measuring the time of flight to a detector that measure collisions. Unlike mass spectrometry, the method of the present invention does not require the extreme sensitivity required to differentiate between very small mass differences in large molecules. The present invention is therefore more robust than the prior art and well suited for extremely high throughput sequencing of large nucleic acid molecules.