The best replacement for encode is encrypt.

The best alternatives to encode are rated as following:
★★★★★  encrypt
★★★★  transcode
★★★  decode
★★★  code
★  better quality
★  remux
★  audiophile
★  decode video
  serialize
  decode base64
  bitstream

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

Other search terms related to encode and their ratings are:
★★★★★ handbrake
★★★★ x264
You have in mind a companion for encode and it is not yet here? Propose!



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encode
encrypt
transcode