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Commits on Jan 10, 2025

• Improve report figure to display more combinations of trimmers and aligners better. This adds a --seperate flag to report which splits figure report plots into seperate pages

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Commits on Jan 8, 2025

• Make modify-busco script also copy refes_db file for metaeuk BUSCO mode

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• Update minimal example to be compatible with BUSCO5 and latest changes of phylociraptor

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  80e69d6

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• Update modify-busco script to also account for correct naming scheme of busco5 sets (_odb10 suffix)

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  1a1fb0e

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• Remove possibly confusing CLI output from modify busco script

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Commits on Dec 20, 2024

• Fix problem with report and the busco summary file when orthofinder is used

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Commits on Dec 13, 2024

• Fix where speciestree searches for orthologs

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• Fix where modeltest searches for ortholog files

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Commits on Nov 29, 2024

• Fix where busco wildcard is taken from.

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• Fix which hash is used in get_aln_stats with BUSCO

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Commits on Nov 20, 2024

• Attempt to fix display of Orthofinder results in report

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  b1a4cda

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• Another fix to where single copy orthologs are stored.

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• Name all code chunks in report

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  883a263

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• Fix problem with different location of single copy ortholog files in orthofinder and busco mode

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Commits on Nov 12, 2024

• Set aaa filter correctly and fix creating outfiles for orthofinder filter-orthology

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• Fix another typo in create_sequence_files.py

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  c24c710

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• Fix typo in create_sequence_files.py

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• Fix typo in create_sequence_files.py

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• Make sure minsp is correctly applied in orthofinder mode

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Commits on Oct 15, 2024

• Add missing untrimmed rulefile

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• Make possibility for skipping modeltest easier to use

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Commits on Oct 14, 2024

• Put yaml file loading in one central place for all parts of phylociraptor(libphylciraptor.filehandling). This makes it easier to change how the yaml config file is parsed.

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Commits on Oct 11, 2024

• Add possibility to bypass trimming

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• Fix phylociraptor check for filter-align

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• Add check for missing option fields also in two additional places

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  41ebef4

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• Update Hashing to fill in missing option values for align, filter-align and modeltest. Make debug output more clear

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Commits on Oct 10, 2024

• Add correct clipkit paramater return

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Commits on Sep 24, 2024

• Enable theme again for rtd

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  6a4d569

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• Fix typo in index.rst

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• Disable theme in attempt to fix rtd

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• Add missing requirements file

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• Additional changes to fix readthedocs build

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  c09b402

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• Merge pull request #36 from reslp/orthofinder

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• Add readthedocs config to be able to build docs again

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Commits on Sep 23, 2024

• Add PRANK to list of aligners

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