The best replacement for punnett square is pedigree.

The best alternatives to punnett square are rated as following:
★★★★★  pedigree
★★★  testcross

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Speaking about punnett square, one probably shouldn't forget about incomplete dominance.

Other search terms related to punnett square and their ratings are:
★★★★★ incomplete dominance
★★★ genotype and phenotype
★ codominance
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punnett square
pedigree
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