The best replacement for gel electrophoresis is paper chromatography.

The best alternatives to gel electrophoresis are rated as following:
★★★★★  paper chromatography
★★  western blot
★★  chromatography
★  sds page
★  southern blotting
★  capillary electrophoresis
★  capillary
★  agarose gel electrophoresis
  agarose
  sds gel
  thin layer chromatography
  native gel electrophoresis
  agarose gel

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Speaking about gel electrophoresis, one probably shouldn't forget about restriction enzymes.

Other search terms related to gel electrophoresis and their ratings are:
★★★★★ restriction enzymes
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gel electrophoresis
paper chromatography
western blot