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Commits on Jan 1, 2026

• Update NOTICE copyright year

  brunocontrerasmoreira

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Commits on Dec 23, 2025

• added video

  eead-csic-compbio

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• added 2026 rice paper

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Commits on Sep 4, 2025

• Merge branch 'master' of https://github.com/Ensembl/plant-scripts

  eead-csic-compbio

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• updated date, imported in AlloSHP

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Commits on Aug 28, 2025

• Merge pull request #16 from brunocontrerasmoreira/master

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• fixed blank

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  brunocontrerasmoreira

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  JAlvarezJarreta

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• Ensembl is enough

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  brunocontrerasmoreira

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  JAlvarezJarreta

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• Ensembl is enough

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  brunocontrerasmoreira

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  JAlvarezJarreta

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  34d33aa

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• fixed blanks

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  brunocontrerasmoreira

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  JAlvarezJarreta

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  4dfdce1

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• removed code for parsing split TSV file

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  brunocontrerasmoreira

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  JAlvarezJarreta

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• indented example

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  brunocontrerasmoreira

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  JAlvarezJarreta

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Commits on Aug 27, 2025

• retested on Ensembl Plants 61

  eead-csic-compbio

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• sub get_gene_coords_GTF_file can handle long chr names

  eead-csic-compbio

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• retested

  eead-csic-compbio

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• adapted to all-vs-all TSV file

  eead-csic-compbio

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• # NOTE: tries only the bulky all-vs-all file (GBs)

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Commits on Jul 16, 2025

• Merge pull request #15 from shradhaebi/add/scripts

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• Added README and other files

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Commits on Jul 11, 2025

• Adding scripts to merge genes

  shradhaebi

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Commits on May 29, 2025

• example rename_pangenes.pl output

  eead-csic-compbio

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Commits on May 28, 2025

• explained rename_pangenes.pl

  eead-csic-compbio

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• example long gene model (figure 13)

  eead-csic-compbio

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• explained missing, split and long gene models (figure 12)

  eead-csic-compbio

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Commits on May 27, 2025

• updated table of global vars

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• dont print global MAXDISTNEIGHBORS

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• _cluster_analysis.pl -t now affects pangene set growth simulation

  eead-csic-compbio

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• _cluster_analysis.pl -t now affects pangene set growth simulation

  eead-csic-compbio

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• -t now affects pangene set growth simulation

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Commits on May 19, 2025

• check_quality.pl cant assume gff files are available

  eead-csic-compbio

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• dont assume gff files are available

  eead-csic-compbio

  committed
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Commits on May 14, 2025

• added POCS to troubleshooting to explain small cores

  brunocontrerasmoreira

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• added POCS to troubleshooting to explain small cores

  eead-csic-compbio

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Commits on Apr 8, 2025

• apt update before installs

  eead-csic-compbio

  committed
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• updated TSV header

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