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1. Commits on Oct 20, 2026

   • GFF3_utils2: index genes in coordinate order so output order is reproducible

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   • Fasta_reader: skip text before the first header instead of reading it as a sequence

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   • Minimum ORF length 50 aa with a frame-contrast test for ORFs under 100 codons

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   • Start refinement: Kozak evidence enters the keep-or-trim cutoff additively

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2. Commits on Oct 19, 2026

   • Kozak model training in its own step (train_kozak_model.pl) with a sequence logo

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   • Start refinement by frame contrast and Kozak context; single best ORF per transcript by default; length retention only for TAA/TAG/TGA codes

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3. Commits on Oct 18, 2026

   • Skip start refinement when there are too few training starts; use the selected genetic code in the training redundancy filter

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     brianjohnhaas

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4. Commits on Oct 17, 2026

   • Long-ORF retention thresholds from a regenerated random-sequence simulation

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   • Exclude the terminal stop of the selected genetic code from Markov training and scoring

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   • Genome propagation gene ids, option alias and usage-text corrections

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   • Start refinement: score candidates on the same window and scale used to train the threshold

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5. Commits on Mar 20, 2026

   • dockerfile updated for v6.0.0

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   • setting version 6.0.0

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   • Update versioning and drop DB_File from Dockerfile

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   • Add TransDecoder pipeline wrapper script

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   • Update README.md

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6. Commits on Mar 19, 2026

   • permission change

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7. Commits on Sep 29, 2025

   • removed cufflinks from message

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8. Commits on Aug 26, 2025

   • no stderr blankline

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   • not printing the track line

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   • avoid duplicating bed lines in output

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9. Commits on Oct 2, 2024

   • Merge pull request #202 from colindaven/patch-1

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   • solve hmmer download by getting specific version

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10. Commits on Mar 22, 2024

    • Update README.md

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11. Commits on Sep 13, 2023

    • Merge pull request #184 from mr-c/fix_test_paths

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    • Fix some test paths

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    • Merge pull request #183 from mr-c/python3

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    • Use 2to3 to port from Python2 to Python3

      

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12. Commits on Jul 16, 2023

    • changelog update for v5.7.1

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    • docker tests included for v5.7.1

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    • add test docker

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    • update for docker test

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    • version 5.7.1

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    • rigorous definition around workdir based on output directory, needed for docker

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13. Commits on May 24, 2023

    • adding blast and hammer to the docker

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