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Upgrade to pyham 2 and ete4, make --species_tree optional - #48

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alpae merged 6 commits into
DessimozLab:mainfrom
alpae:pyham2
Oct 23, 2026
Merged

alpae merged 6 commits into
DessimozLab:mainfrom
alpae:pyham2

Merge remote-tracking branch 'upstream/main' into pyham2

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GitGuardian / GitGuardian Security Checks succeeded Oct 23, 2026 in 43s

No secrets detected ✅

6 commits were scanned without uncovering any secrets.

Details

Commits scanned: 6

  • Pull request #48: pyham2 👉 main

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