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Update to v1.50 #29

Merged
merged 12 commits into from
Oct 22, 2023
Merged

Update to v1.50 #29

merged 12 commits into from
Oct 22, 2023

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raufs
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@raufs raufs commented Oct 22, 2023

  • Change-up handling of genes which were placed in coarse ortholog groups by OrthoFinder but are dropped off in the more resolved hierarchical ortholog groups. Instead of grouping the remaining genes into a bin identified by their original coarse (OG) names. Based on Some clarification on xenologues and putative HGT davidemms/OrthoFinder#288 , lsaBGC (lsaBGC-Ready specifically) will now parse the genes listed per genome in the Phylogenetically_Misplaced_Genes/ directory to and match them to their closest HOGs based on the relations with other genes reported in the Putative_Xenologs/ directory. The remaining "misplaced" genes will just be treated as singleton ortholog groups.
  • Introduce Panaroo (🐀 ) as an option for determining ortholog groups - most appropriate for single bacterial species or lineages! 🎊
  • Update docker images to install older setuptools to avoid deprecation warning (temporary solution :/)

@raufs raufs merged commit b731ae0 into main Oct 22, 2023
@raufs raufs deleted the develop-v1.40 branch November 28, 2023 03:14
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