The best replacement for jks is jceks.

The best alternatives to jks are rated as following:
★★★★★  jceks
★★★★★  pkcs12
★★  jka
★  pkcs
  kdb
  currie
  p12

Your alternative for jks is not listed? Suggest!
Speaking about jks, one probably shouldn't forget about openssl.

Other search terms related to jks and their ratings are:
★★★★★ openssl
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