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[WIP] Add TSV output from monophylizer.pl script#6

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rvosa merged 3 commits into
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copilot/add-tsv-output-from-script
Dec 12, 2025
Merged

[WIP] Add TSV output from monophylizer.pl script#6
rvosa merged 3 commits into
masterfrom
copilot/add-tsv-output-from-script

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Copilot AI commented Dec 12, 2025

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Task: Use monophylizer.pl script to make TSV output from ML_Argyresthiidae.nwk and add it to the folder

Progress Checklist:

  • Explore repository structure and understand monophylizer.pl script
  • Install Bio::Phylo dependency (version 2.0.2)
  • Test monophylizer.pl script with ML_Argyresthiidae.nwk file
  • Verify script generates correct TSV output
  • Create data/tsv folder for TSV outputs
  • Generate and save ML_Argyresthiidae.tsv file (31 lines: 1 header + 30 species)
  • Verify the TSV file is correctly formatted
  • Address code review comments (removed trailing newline)
  • Run security check (passed - no code changes)

Summary:

Successfully created ML_Argyresthiidae.tsv file in data/tsv/ folder using the monophylizer.pl script. The TSV contains monophyly assessment results for 30 species from the Argyresthiidae family, showing 28 monophyletic species and 2 paraphyletic species (Argyresthia semifusca and Argyresthia semitestacella).

Original prompt

Use the monophylizer.pl script to make a TSV output from ML_Argyresthiidae.nwk and add it to the folder


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Copilot AI and others added 2 commits December 12, 2025 20:24
Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
@rvosa rvosa marked this pull request as ready for review December 12, 2025 20:27
@rvosa rvosa merged commit 5ce04a3 into master Dec 12, 2025
10 checks passed
Copilot AI requested a review from rvosa December 12, 2025 20:27
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2 participants