Address Biopython deprecation warnings

[victorlin]

Description of proposed changes

See commit messages.

Related issue(s)

• ancestral, translate: GFF parsing broken with Biopython >=1.82 #1373

Checklist

• Checks pass (expected failure with 05bff35, succces with a3df38d)
• If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (ad4ed1b) 66.13% compared to head (a3df38d) 66.14%.

❗ Current head a3df38d differs from pull request most recent head 2553d4e. Consider uploading reports for the commit 2553d4e to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1379      +/-   ##
==========================================
+ Coverage   66.13%   66.14%   +0.01%     
==========================================
  Files          68       68              
  Lines        7222     7225       +3     
  Branches     1777     1777              
==========================================
+ Hits         4776     4779       +3     
  Misses       2177     2177              
  Partials      269      269              

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